Emerging Technologies for Gut Microbiome Research
Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and...
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Published in | Trends in microbiology (Regular ed.) Vol. 24; no. 11; pp. 887 - 901 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
England
Elsevier Ltd
01.11.2016
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Subjects | |
Online Access | Get full text |
ISSN | 0966-842X 1878-4380 1878-4380 |
DOI | 10.1016/j.tim.2016.06.008 |
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Abstract | Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies.
Compositional and functional analyses of the gut microbiome by next-generation sequencing methods have completely transformed research approaches to determine microbial species and their role in human health and disease.
New culturing technologies facilitate mechanistic studies of difficult-to-culture gut microbes. A number of previously uncultivable microbes are now cultivable as a result of these advancements, providing insight into community dynamics and network interactions.
Stem cell technologies and tissue engineering allow for construction of organoids capable of facilitating cost-effective, high-throughput microbiome studies.
Modulation of the gut microbiota is emerging as an effective method to delineate composition and function of microbial communities, providing new methods to prevent and treat disease. |
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AbstractList | Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies. Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches will improve the efficiency and quality of microbiome research. Here, we will discuss emerging technologies and their potential impact on gut microbiome studies. Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies.Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies. Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies. Compositional and functional analyses of the gut microbiome by next-generation sequencing methods have completely transformed research approaches to determine microbial species and their role in human health and disease. New culturing technologies facilitate mechanistic studies of difficult-to-culture gut microbes. A number of previously uncultivable microbes are now cultivable as a result of these advancements, providing insight into community dynamics and network interactions. Stem cell technologies and tissue engineering allow for construction of organoids capable of facilitating cost-effective, high-throughput microbiome studies. Modulation of the gut microbiota is emerging as an effective method to delineate composition and function of microbial communities, providing new methods to prevent and treat disease. |
Author | Arnold, Jason W. Roach, Jeffrey Azcarate-Peril, M. Andrea |
AuthorAffiliation | 1 Department of Cell Biology and Physiology, and Microbiome Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC 2 Research Computing, University of North Carolina, Chapel Hill, NC |
AuthorAffiliation_xml | – name: 1 Department of Cell Biology and Physiology, and Microbiome Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC – name: 2 Research Computing, University of North Carolina, Chapel Hill, NC |
Author_xml | – sequence: 1 givenname: Jason W. surname: Arnold fullname: Arnold, Jason W. organization: Department of Cell Biology and Physiology, and Microbiome Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC, USA – sequence: 2 givenname: Jeffrey surname: Roach fullname: Roach, Jeffrey organization: Research Computing, University of North Carolina, Chapel Hill, NC, USA – sequence: 3 givenname: M. Andrea surname: Azcarate-Peril fullname: Azcarate-Peril, M. Andrea email: azcarate@med.unc.edu organization: Department of Cell Biology and Physiology, and Microbiome Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC, USA |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27426971$$D View this record in MEDLINE/PubMed |
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Cites_doi | 10.1079/BJN/2002539 10.1371/journal.pone.0030126 10.1017/S0007114514001135 10.1016/j.cmet.2014.10.002 10.3181/00379727-108-27055 10.1073/pnas.1409644111 10.1016/j.ijmm.2016.03.005 10.4161/gmic.22371 10.4103/0971-5916.162091 10.1097/MOG.0b013e328365d365 10.1111/jam.12105 10.7717/peerj.593 10.1155/2015/326032 10.4161/gmic.2.4.16332 10.1097/01.mpg.0000189346.25172.fd 10.1007/s10295-010-0831-5 10.2174/1381612054546932 10.1126/scitranslmed.3000322 10.2174/1871528113666140623113221 10.1371/journal.pone.0147210 10.1016/0003-9969(64)90069-X 10.1038/nature11552 10.1053/j.gastro.2014.01.004 10.1186/s12864-015-1781-0 10.1371/journal.pone.0073140 10.1111/1574-6941.12187 10.1128/AAC.31.8.1231 10.3945/an.114.007450 10.1038/nprot.2010.18 10.1038/ismej.2014.117 10.1111/1751-7915.12366 10.1126/scitranslmed.3008051 10.1136/bmjopen-2014-005047 10.1039/c3ib40126j 10.1097/BOR.0000000000000191 10.1038/nrgastro.2015.47 10.1371/journal.pone.0017447 10.1016/j.cmet.2014.10.003 10.1017/S0007114515000823 10.1128/AEM.01754-09 10.1128/AEM.02977-13 10.3402/mehd.v25.23062 10.1016/j.csbj.2015.06.001 10.1152/ajpgi.00110.2011 10.1093/nar/gkh063 10.1038/nature10213 10.1111/2041-210X.12114 10.1099/13500872-141-2-513 10.1007/s00281-014-0457-1 10.1016/j.femsec.2004.05.002 10.1016/j.mam.2012.11.001 10.1371/journal.pone.0148698 10.1159/000358465 10.1016/S0167-7012(03)00059-9 10.1126/science.1110591 10.1038/nature11053 10.1126/science.1234852 10.3791/52154 10.1136/archdischild-2012-302119 10.1146/annurev-biophys-051013-022916 10.1016/j.febslet.2014.03.035 10.1038/ismej.2010.110 10.1038/nrmicro2853 10.1128/IAI.02561-14 10.1101/gr.107987.110 10.1111/j.1753-4887.2012.00505.x 10.1186/1475-2859-13-S1-S7 10.1073/pnas.1102938108 10.1097/MCO.0000000000000209 10.1016/j.pharmthera.2016.04.007 10.1016/j.cels.2015.08.013 10.1073/pnas.1522193112 10.1016/j.mib.2015.08.003 10.1128/AEM.68.8.3878-3885.2002 10.1101/gr.165845.113 10.3892/mmr.2015.4124 10.1080/07315724.2013.878232 10.1016/j.cell.2014.09.022 10.1073/pnas.1319284111 10.1371/journal.pone.0032118 10.1038/nmeth.3869 10.1038/ncb3104 10.1038/nature09199 10.1128/AEM.01541-09 10.1186/1471-2407-8-310 10.1101/gad.212522.112 10.1371/journal.pbio.1001377 10.1126/science.1124234 10.1016/j.chom.2015.09.002 10.1038/nmeth.f.303 10.1016/j.cmet.2015.07.001 10.1136/gutjnl-2015-309618 10.4093/dmj.2015.39.3.198 10.1128/AAC.00602-12 10.1371/journal.pone.0016393 10.1038/nbt.2676 10.1371/journal.pone.0012191 10.1016/j.mimet.2014.11.007 10.1039/c2lc40074j 10.1002/mas.20032 10.1111/j.1365-2249.2007.03522.x 10.1371/journal.pone.0138135 10.1038/nrmicro2297 10.1186/s40168-015-0101-x 10.1038/nmeth.2066 10.1128/IAI.00161-15 10.1038/nbt.2857 10.1038/nature12820 10.1038/nprot.2013.137 10.1073/pnas.1514285112 10.1186/1475-2859-11-161 10.2174/138920211797248619 10.1128/AEM.64.2.651-658.1998 10.1371/journal.pone.0125448 10.1080/19490976.2015.1039223 10.1126/scitranslmed.aab2009 10.1039/C3LC51353J 10.1016/j.ijmm.2004.06.023 10.1053/j.gastro.2014.01.049 10.1007/s00394-014-0689-9 10.1371/journal.pcbi.1002358 10.1146/annurev.mi.31.100177.000543 10.3920/BM2015.0114 10.1016/j.chom.2014.02.005 10.2174/18715273113126660147 10.1371/journal.pone.0034242 10.1038/nature11209 |
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References | Faith (bib1190) 2010; 4 Azcarate-Peril (bib1055) 2011; 2 Bach Knudsen (bib0720) 2015; 6 Watson (bib1310) 2013; 114 Azcarate-Peril (bib1030) 2011; 301 Rhodes (bib1080) 1998; 64 Segata (bib0825) 2012; 9 Kostic (bib1240) 2013; 27 Bindels (bib0960) 2015; 12 Meike Samtlebe (bib0970) 2016; 68 Kim (bib1245) 2012; 12 Ladirat (bib0910) 2014; 87 Gevers (bib0695) 2014; 15 Adamberg (bib1220) 2014 Shen (bib1020) 2013; 34 Franzosa (bib1160) 2014; 111 Hur, Lee (bib0950) 2015; 39 Holmes (bib0815) 2012; 7 Savage (bib0680) 1977; 31 Murphy (bib1290) 2015; 18 Reyes (bib0925) 2012; 10 Kanehisa (bib1145) 2004; 32 El Aidy, Kleerebezem (bib0715) 2013; 29 Joice (bib0840) 2014; 20 Eren (bib0810) 2014; 111 Kim, Ingber (bib0880) 2013; 5 Santiago-Rodriguez (bib1090) 2015; 10 Huse (bib1110) 2012; 7 Stewart (bib1065) 2013; 98 Mills (bib1140) 2013; 4 Earle (bib1235) 2015; 18 Hollister (bib1150) 2015; 3 Tremaroli, Backhed (bib0685) 2012; 489 Dechesne (bib0700) 2016; 9 Parker, Snyder (bib1050) 1961; 108 Li (bib1105) 2012; 7 Blaut (bib1075) 2002; 87 Yatsunenko (bib1295) 2012; 486 Bikel (bib0845) 2015; 13 Ando (bib0775) 2015; 1 Eckburg (bib1040) 2005; 308 Petrof, Khoruts (bib0745) 2014; 146 Gueimonde (bib0920) 2006; 42 Jung (bib1210) 2014; 90 Gibbons (bib1045) 1964; 9 Monteagudo-Mera (bib1320) 2016; 7 Gosalbes (bib1155) 2011; 6 Sierra (bib0900) 2015; 54 Ladirat (bib1305) 2014; 112 Tikhonov (bib0795) 2015; 9 Vandeputte (bib0820) 2016; 65 Medina (bib1005) 2007; 150 Tang (bib0735) 2011; 12 Forbester (bib0890) 2015; 83 Villas-Boas (bib1180) 2005; 24 MacFabe (bib0725) 2015; 26 Pusch, Kostrzewa (bib0730) 2005; 11 Englert (bib1255) 2010; 5 Langille (bib0830) 2013; 31 Hiergeist, Reischl (bib0705) 2016 Rusconi (bib1250) 2014; 43 Sato, Clevers (bib0865) 2013; 340 Kang (bib0940) 2015; 7 Panzer, Lynch (bib0690) 2015; 27 Connon, Giovannoni (bib0740) 2002; 68 Weingarden (bib0965) 2016; 11 Huttenhower (bib1035) 2014; 159 David (bib1270) 2014; 505 Gao (bib1325) 2015; 12 Silva (bib0915) 1987; 31 Caporaso (bib1095) 2010; 7 Neu (bib0760) 2014; 110 Giovannini (bib0905) 2014; 33 Ohtani (bib0955) 2015; 37 Donskey (bib1060) 2003; 54 Nichols (bib1205) 2010; 76 Possemiers (bib1225) 2004; 49 Kim (bib0885) 2016; 113 McFarland (bib0765) 2014; 4 Sobhani (bib0985) 2011; 6 Lee (bib1010) 2008; 8 McDonald (bib1230) 2015; 108 Walsh (bib1285) 2014; 588 Huang (bib0750) 2015; 27 Shoaie (bib1280) 2015; 22 Schloss (bib0785) 2009; 75 Methé (bib1100) 2012; 486 Faith (bib1195) 2014; 6 Hidalgo-Cantabrana (bib1015) 2014; 80 Actis (bib0755) 2014; 13 Abubucker (bib0835) 2012; 8 Maura (bib1345) 2012; 56 Leslie (bib0895) 2015; 83 Eren (bib0805) 2013 Hraiech (bib1350) 2015; 9 Naseer (bib1025) 2014; 13 Foca, Liberto (bib1135) 2015 Gevers (bib0855) 2012; 10 Fogh, Trempe (bib0875) 1975 Turnbaugh (bib1200) 2009; 1 Herold (bib0930) 2004; 294 Allegretti (bib0780) 2014 Gracz (bib1265) 2015; 17 Callahan (bib0800) 2016; 13 Gill (bib1000) 2006; 312 Camp (bib1170) 2014; 24 Kabeerdoss (bib0995) 2015; 142 Carding (bib0990) 2015; 26 Goodman (bib1185) 2011; 108 Candon (bib1340) 2015; 10 Reyes (bib1125) 2015; 112 Kau (bib0980) 2011; 474 O’Donnell (bib1115) 2016; 11 de Vos, de Vos (bib0975) 2012; 70 Huh (bib0870) 2013; 8 Schuppler (bib1070) 1995; 141 Palmero (bib1120) 2011; 38 Morgan, Huttenhower (bib0710) 2014; 146 Segers, Lebeer (bib0770) 2014; 13 Lebeer (bib1335) 2010; 8 Santiago-Rodriguez (bib1165) 2015; 16 Manichanh (bib0935) 2010; 20 Reyes (bib1130) 2010; 466 Vandenplas (bib1315) 2015; 113 Claes (bib1330) 2012; 11 Miller (bib1085) 1956; 68 Devine (bib0860) 2013; 8 Wang (bib1260) 2014; 14 Degnan (bib1300) 2014; 20 Wang (bib1215) 2014; 32 Mahé (bib0790) 2014; 2 Allali (bib0850) 2015; 6 Ding (bib1275) 2010; 5 Sivaprakasam (bib1175) 2016 Drumo (bib0945) 2015; 5 Villas-Boas (10.1016/j.tim.2016.06.008_bib1180) 2005; 24 Tang (10.1016/j.tim.2016.06.008_bib0735) 2011; 12 Medina (10.1016/j.tim.2016.06.008_bib1005) 2007; 150 Sierra (10.1016/j.tim.2016.06.008_bib0900) 2015; 54 Drumo (10.1016/j.tim.2016.06.008_bib0945) 2015; 5 Kim (10.1016/j.tim.2016.06.008_bib0885) 2016; 113 Reyes (10.1016/j.tim.2016.06.008_bib0925) 2012; 10 Actis (10.1016/j.tim.2016.06.008_bib0755) 2014; 13 Ohtani (10.1016/j.tim.2016.06.008_bib0955) 2015; 37 Gueimonde (10.1016/j.tim.2016.06.008_bib0920) 2006; 42 Kanehisa (10.1016/j.tim.2016.06.008_bib1145) 2004; 32 Schloss (10.1016/j.tim.2016.06.008_bib0785) 2009; 75 Hur (10.1016/j.tim.2016.06.008_bib0950) 2015; 39 Huttenhower (10.1016/j.tim.2016.06.008_bib1035) 2014; 159 Li (10.1016/j.tim.2016.06.008_bib1105) 2012; 7 Vandenplas (10.1016/j.tim.2016.06.008_bib1315) 2015; 113 Miller (10.1016/j.tim.2016.06.008_bib1085) 1956; 68 Allali (10.1016/j.tim.2016.06.008_bib0850) 2015; 6 Methé (10.1016/j.tim.2016.06.008_bib1100) 2012; 486 Meike Samtlebe (10.1016/j.tim.2016.06.008_bib0970) 2016; 68 Joice (10.1016/j.tim.2016.06.008_bib0840) 2014; 20 Devine (10.1016/j.tim.2016.06.008_bib0860) 2013; 8 Hiergeist (10.1016/j.tim.2016.06.008_bib0705) 2016 Gosalbes (10.1016/j.tim.2016.06.008_bib1155) 2011; 6 Bikel (10.1016/j.tim.2016.06.008_bib0845) 2015; 13 Possemiers (10.1016/j.tim.2016.06.008_bib1225) 2004; 49 Gevers (10.1016/j.tim.2016.06.008_bib0695) 2014; 15 Foca (10.1016/j.tim.2016.06.008_bib1135) 2015 Panzer (10.1016/j.tim.2016.06.008_bib0690) 2015; 27 Kim (10.1016/j.tim.2016.06.008_bib1245) 2012; 12 Hidalgo-Cantabrana (10.1016/j.tim.2016.06.008_bib1015) 2014; 80 Vandeputte (10.1016/j.tim.2016.06.008_bib0820) 2016; 65 O’Donnell (10.1016/j.tim.2016.06.008_bib1115) 2016; 11 McDonald (10.1016/j.tim.2016.06.008_bib1230) 2015; 108 Tremaroli (10.1016/j.tim.2016.06.008_bib0685) 2012; 489 Santiago-Rodriguez (10.1016/j.tim.2016.06.008_bib1165) 2015; 16 Langille (10.1016/j.tim.2016.06.008_bib0830) 2013; 31 Blaut (10.1016/j.tim.2016.06.008_bib1075) 2002; 87 Englert (10.1016/j.tim.2016.06.008_bib1255) 2010; 5 Watson (10.1016/j.tim.2016.06.008_bib1310) 2013; 114 Kau (10.1016/j.tim.2016.06.008_bib0980) 2011; 474 Earle (10.1016/j.tim.2016.06.008_bib1235) 2015; 18 Claes (10.1016/j.tim.2016.06.008_bib1330) 2012; 11 Wang (10.1016/j.tim.2016.06.008_bib1260) 2014; 14 Lee (10.1016/j.tim.2016.06.008_bib1010) 2008; 8 Neu (10.1016/j.tim.2016.06.008_bib0760) 2014; 110 Segers (10.1016/j.tim.2016.06.008_bib0770) 2014; 13 Forbester (10.1016/j.tim.2016.06.008_bib0890) 2015; 83 David (10.1016/j.tim.2016.06.008_bib1270) 2014; 505 Silva (10.1016/j.tim.2016.06.008_bib0915) 1987; 31 Rusconi (10.1016/j.tim.2016.06.008_bib1250) 2014; 43 Jung (10.1016/j.tim.2016.06.008_bib1210) 2014; 90 Gill (10.1016/j.tim.2016.06.008_bib1000) 2006; 312 El Aidy (10.1016/j.tim.2016.06.008_bib0715) 2013; 29 Azcarate-Peril (10.1016/j.tim.2016.06.008_bib1030) 2011; 301 Parker (10.1016/j.tim.2016.06.008_bib1050) 1961; 108 Huh (10.1016/j.tim.2016.06.008_bib0870) 2013; 8 Leslie (10.1016/j.tim.2016.06.008_bib0895) 2015; 83 Fogh (10.1016/j.tim.2016.06.008_bib0875) 1975 Turnbaugh (10.1016/j.tim.2016.06.008_bib1200) 2009; 1 Holmes (10.1016/j.tim.2016.06.008_bib0815) 2012; 7 Sivaprakasam (10.1016/j.tim.2016.06.008_bib1175) 2016 McFarland (10.1016/j.tim.2016.06.008_bib0765) 2014; 4 Eren (10.1016/j.tim.2016.06.008_bib0810) 2014; 111 Maura (10.1016/j.tim.2016.06.008_bib1345) 2012; 56 Ando (10.1016/j.tim.2016.06.008_bib0775) 2015; 1 Monteagudo-Mera (10.1016/j.tim.2016.06.008_bib1320) 2016; 7 Faith (10.1016/j.tim.2016.06.008_bib1190) 2010; 4 Shen (10.1016/j.tim.2016.06.008_bib1020) 2013; 34 Walsh (10.1016/j.tim.2016.06.008_bib1285) 2014; 588 Huang (10.1016/j.tim.2016.06.008_bib0750) 2015; 27 Gibbons (10.1016/j.tim.2016.06.008_bib1045) 1964; 9 Murphy (10.1016/j.tim.2016.06.008_bib1290) 2015; 18 Reyes (10.1016/j.tim.2016.06.008_bib1130) 2010; 466 Giovannini (10.1016/j.tim.2016.06.008_bib0905) 2014; 33 Ding (10.1016/j.tim.2016.06.008_bib1275) 2010; 5 Donskey (10.1016/j.tim.2016.06.008_bib1060) 2003; 54 Mills (10.1016/j.tim.2016.06.008_bib1140) 2013; 4 Connon (10.1016/j.tim.2016.06.008_bib0740) 2002; 68 Stewart (10.1016/j.tim.2016.06.008_bib1065) 2013; 98 Manichanh (10.1016/j.tim.2016.06.008_bib0935) 2010; 20 Kabeerdoss (10.1016/j.tim.2016.06.008_bib0995) 2015; 142 Hollister (10.1016/j.tim.2016.06.008_bib1150) 2015; 3 Degnan (10.1016/j.tim.2016.06.008_bib1300) 2014; 20 Bach Knudsen (10.1016/j.tim.2016.06.008_bib0720) 2015; 6 Abubucker (10.1016/j.tim.2016.06.008_bib0835) 2012; 8 Santiago-Rodriguez (10.1016/j.tim.2016.06.008_bib1090) 2015; 10 Goodman (10.1016/j.tim.2016.06.008_bib1185) 2011; 108 Carding (10.1016/j.tim.2016.06.008_bib0990) 2015; 26 Segata (10.1016/j.tim.2016.06.008_bib0825) 2012; 9 Dechesne (10.1016/j.tim.2016.06.008_bib0700) 2016; 9 Kang (10.1016/j.tim.2016.06.008_bib0940) 2015; 7 Morgan (10.1016/j.tim.2016.06.008_bib0710) 2014; 146 Franzosa (10.1016/j.tim.2016.06.008_bib1160) 2014; 111 Mahé (10.1016/j.tim.2016.06.008_bib0790) 2014; 2 Gracz (10.1016/j.tim.2016.06.008_bib1265) 2015; 17 Reyes (10.1016/j.tim.2016.06.008_bib1125) 2015; 112 Petrof (10.1016/j.tim.2016.06.008_bib0745) 2014; 146 Shoaie (10.1016/j.tim.2016.06.008_bib1280) 2015; 22 de Vos (10.1016/j.tim.2016.06.008_bib0975) 2012; 70 Herold (10.1016/j.tim.2016.06.008_bib0930) 2004; 294 Wang (10.1016/j.tim.2016.06.008_bib1215) 2014; 32 Faith (10.1016/j.tim.2016.06.008_bib1195) 2014; 6 Candon (10.1016/j.tim.2016.06.008_bib1340) 2015; 10 Ladirat (10.1016/j.tim.2016.06.008_bib0910) 2014; 87 Bindels (10.1016/j.tim.2016.06.008_bib0960) 2015; 12 Nichols (10.1016/j.tim.2016.06.008_bib1205) 2010; 76 Azcarate-Peril (10.1016/j.tim.2016.06.008_bib1055) 2011; 2 Hraiech (10.1016/j.tim.2016.06.008_bib1350) 2015; 9 Yatsunenko (10.1016/j.tim.2016.06.008_bib1295) 2012; 486 Lebeer (10.1016/j.tim.2016.06.008_bib1335) 2010; 8 Pusch (10.1016/j.tim.2016.06.008_bib0730) 2005; 11 Sato (10.1016/j.tim.2016.06.008_bib0865) 2013; 340 Rhodes (10.1016/j.tim.2016.06.008_bib1080) 1998; 64 MacFabe (10.1016/j.tim.2016.06.008_bib0725) 2015; 26 Tikhonov (10.1016/j.tim.2016.06.008_bib0795) 2015; 9 Caporaso (10.1016/j.tim.2016.06.008_bib1095) 2010; 7 Camp (10.1016/j.tim.2016.06.008_bib1170) 2014; 24 Weingarden (10.1016/j.tim.2016.06.008_bib0965) 2016; 11 Eckburg (10.1016/j.tim.2016.06.008_bib1040) 2005; 308 Huse (10.1016/j.tim.2016.06.008_bib1110) 2012; 7 Naseer (10.1016/j.tim.2016.06.008_bib1025) 2014; 13 Schuppler (10.1016/j.tim.2016.06.008_bib1070) 1995; 141 Kostic (10.1016/j.tim.2016.06.008_bib1240) 2013; 27 Callahan (10.1016/j.tim.2016.06.008_bib0800) 2016; 13 Gevers (10.1016/j.tim.2016.06.008_bib0855) 2012; 10 Eren (10.1016/j.tim.2016.06.008_bib0805) 2013 Allegretti (10.1016/j.tim.2016.06.008_bib0780) 2014 Gao (10.1016/j.tim.2016.06.008_bib1325) 2015; 12 Palmero (10.1016/j.tim.2016.06.008_bib1120) 2011; 38 Ladirat (10.1016/j.tim.2016.06.008_bib1305) 2014; 112 Sobhani (10.1016/j.tim.2016.06.008_bib0985) 2011; 6 Adamberg (10.1016/j.tim.2016.06.008_bib1220) 2014 Kim (10.1016/j.tim.2016.06.008_bib0880) 2013; 5 Savage (10.1016/j.tim.2016.06.008_bib0680) 1977; 31 12088520 - Br J Nutr. 2002 May;87 Suppl 2:S203-11 26215258 - BMC Genomics. 2015 Jul 28;16:549 12782380 - J Microbiol Methods. 2003 Aug;54(2):249-56 22699610 - Nature. 2012 Jun 13;486(7402):215-21 24647645 - Lab Chip. 2014 May 7;14(9):1622-31 25045346 - Microb Ecol Health Dis. 2014 Jul 15;25:null 22864264 - Nat Rev Microbiol. 2012 Sep;10(9):607-17 15831718 - Science. 2005 Jun 10;308(5728):1635-8 26351661 - Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11941-6 24100720 - Curr Opin Gastroenterol. 2013 Nov;29(6):621-7 26973885 - Cell Syst. 2015 Sep 23;1(3):187-196 24113786 - Nat Protoc. 2013 Nov;8(11):2135-57 22861807 - Nutr Rev. 2012 Aug;70 Suppl 1:S45-56 22904687 - PLoS Biol. 2012;10(8):e1001377 25462016 - J Microbiol Methods. 2015 Jan;108:36-44 25770259 - Adv Nutr. 2015 Mar 13;6(2):206-13 23817533 - Integr Biol (Camb). 2013 Sep;5(9):1130-40 27052158 - Int J Med Microbiol. 2016 Aug;306(5):334-42 26306392 - Microbiome. 2015 Aug 26;3:36 26244934 - Cell Metab. 2015 Aug 4;22(2):320-31 26950069 - PLoS One. 2016 Mar 07;11(3):e0148698 22719234 - PLoS Comput Biol. 2012;8(6):e1002358 24773019 - Annu Rev Biophys. 2014;43:65-91 3307619 - Antimicrob Agents Chemother. 1987 Aug;31(8):1231-3 25824997 - Nat Rev Gastroenterol Hepatol. 2015 May;12(5):303-10 334036 - Annu Rev Microbiol. 1977;31:107-33 24629344 - Cell Host Microbe. 2014 Mar 12;15(3):382-92 15493821 - Int J Med Microbiol. 2004 Sep;294(2-3):115-21 16101460 - Curr Pharm Des. 2005;11(20):2577-91 23241240 - Microb Cell Fact. 2012 Dec 15;11:161 20820862 - J Ind Microbiol Biotechnol. 2011 Jan;38(1):13-20 16456409 - J Pediatr Gastroenterol Nutr. 2006 Feb;42(2):166-70 26668389 - Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):E7-15 24486053 - Gastroenterology. 2014 May;146(6):1437-1448.e1 24412527 - Gastroenterology. 2014 May;146(6):1573-82 20368178 - Sci Transl Med. 2009 Nov 11;1(6):6ra14 24843156 - Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38 26002029 - Curr Opin Rheumatol. 2015 Jul;27(4):373-80 21436049 - Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6252-7 23426613 - Arch Dis Child Fetal Neonatal Ed. 2013 Jul;98(4):F298-303 25664616 - Nat Cell Biol. 2015 Mar;17(3):340-9 20736229 - Genome Res. 2010 Oct;20(10):1411-9 20383131 - Nat Methods. 2010 May;7(5):335-6 23975157 - Nat Biotechnol. 2013 Sep;31(9):814-21 21408168 - PLoS One. 2011 Mar 08;6(3):e17447 23744940 - Science. 2013 Jun 7;340(6137):1190-4 13486607 - Trans Am Clin Climatol Assoc. 1956-1957;68:51-5; discussion 55-8 23159341 - Mol Aspects Med. 2013 Feb;34(1):39-58 14170653 - Arch Oral Biol. 1964 May-Jun;9:365-70 25875428 - Gut Microbes. 2015;6(3):161-72 22699611 - Nature. 2012 May 09;486(7402):222-7 24336217 - Nature. 2014 Jan 23;505(7484):559-63 24965363 - Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):E2875-84 22719824 - PLoS One. 2012;7(6):e34242 25944980 - Mediators Inflamm. 2015;2015:326032 23022738 - Gut Microbes. 2013 Jan-Feb;4(1):4-16 26213462 - Drug Des Devel Ther. 2015 Jul 16;9:3653-63 26031685 - Microb Ecol Health Dis. 2015 May 29;26:28177 27113407 - Pharmacol Ther. 2016 Aug;164:144-51 14681412 - Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80 22688413 - Nat Methods. 2012 Jun 10;9(8):811-4 26835435 - Front Cell Infect Microbiol. 2016 Jan 22;5:106 19712298 - FEMS Microbiol Ecol. 2004 Sep 1;49(3):495-507 25312952 - Infect Immun. 2015 Jan;83(1):138-45 24953716 - Inflamm Allergy Drug Targets. 2014;13(4):217-23 26356259 - Curr Opin Microbiol. 2015 Oct;27:114-20 25404117 - Semin Immunopathol. 2015 Jan;37(1):65-72 26789728 - PLoS One. 2016 Jan 20;11(1):e0147210 14483927 - Proc Soc Exp Biol Med. 1961 Dec;108:749-52 15389842 - Mass Spectrom Rev. 2005 Sep-Oct;24(5):613-46 25186587 - Microb Cell Fact. 2014 Aug 29;13 Suppl 1:S7 24358444 - Methods Ecol Evol. 2013 Dec 1;4(12):null 17956582 - Clin Exp Immunol. 2007 Dec;150(3):531-8 16741115 - Science. 2006 Jun 2;312(5778):1355-9 22719823 - PLoS One. 2012;7(6):e32118 9464403 - Appl Environ Microbiol. 1998 Feb;64(2):651-8 26839072 - Benef Microbes. 2016;7(2):247-64 25276506 - PeerJ. 2014 Sep 25;2:e593 25157183 - BMJ Open. 2014 Aug 25;4(8):e005047 25440055 - Cell Metab. 2014 Nov 4;20(5):731-41 25078251 - FEMS Microbiol Ecol. 2014 Nov;90(2):417-23 20808947 - PLoS One. 2010 Aug 16;5(8):e12191 21700901 - Am J Physiol Gastrointest Liver Physiol. 2011 Sep;301(3):G401-24 22379393 - Curr Genomics. 2011 Sep;12(6):391-403 21983069 - Gut Microbes. 2011 Jul-Aug;2(4):234-43 23006754 - Antimicrob Agents Chemother. 2012 Dec;56(12):6235-42 26439864 - Cell Host Microbe. 2015 Oct 14;18(4):478-88 20631792 - Nature. 2010 Jul 15;466(7304):334-8 25440056 - Cell Metab. 2014 Nov 4;20(5):769-78 27214047 - Nat Methods. 2016 Jul;13(7):581-3 24123746 - Appl Environ Microbiol. 2014 Jan;80(1):9-18 12147485 - Appl Environ Microbiol. 2002 Aug;68(8):3878-85 25549239 - J Vis Exp. 2014 Dec 08;(94):null 26261163 - Indian J Med Res. 2015 Jul;142(1):23-32 22434367 - Lab Chip. 2012 Jun 21;12(12):2165-74 27166579 - Microb Biotechnol. 2016 Jul;9(4):519-24 26137199 - Comput Struct Biotechnol J. 2015 Jun 09;13:390-401 25012900 - ISME J. 2015 Jan;9(1):68-80 24751628 - World Rev Nutr Diet. 2014;110:167-76 26154278 - Curr Opin Clin Nutr Metab Care. 2015 Sep;18(5):515-20 20173072 - Appl Environ Microbiol. 2010 Apr;76(8):2445-50 23592793 - Genes Dev. 2013 Apr 1;27(7):701-18 7704280 - Microbiology. 1995 Feb;141 ( Pt 2):513-21 22319561 - PLoS One. 2012;7(2):e30126 24681100 - FEBS Lett. 2014 Nov 17;588(22):4120-30 26124989 - Diabetes Metab J. 2015 Jun;39(3):198-203 24015295 - PLoS One. 2013 Aug 27;8(8):e73140 26109103 - Sci Transl Med. 2015 Jun 24;7(293):293ra103 25970503 - PLoS One. 2015 May 13;10(5):e0125448 21677749 - Nature. 2011 Jun 15;474(7351):327-36 25964470 - Infect Immun. 2015 Jul;83(7):2926-34 20664551 - ISME J. 2010 Sep;4(9):1094-8 18950540 - BMC Cancer. 2008 Oct 27;8:310 26422376 - PLoS One. 2015 Sep 30;10(9):e0138135 20431532 - Nat Protoc. 2010 May;5(5):864-72 26069274 - Gut. 2016 Jan;65(1):57-62 25651997 - Microb Ecol Health Dis. 2015 Feb 02;26:26191 19801464 - Appl Environ Microbiol. 2009 Dec;75(23):7537-41 23240984 - J Appl Microbiol. 2013 Apr;114(4):1132-46 24963153 - Genome Res. 2014 Sep;24(9):1504-16 24452263 - Sci Transl Med. 2014 Jan 22;6(220):220ra11 25303518 - Cell. 2014 Oct 9;159(2):227-30 24705516 - Nat Biotechnol. 2014 May;32(5):473-8 22972297 - Nature. 2012 Sep 13;489(7415):242-9 26238090 - Mol Med Rep. 2015 Oct;12(4):6119-27 23909489 - FEMS Microbiol Ecol. 2014 Jan;87(1):41-51 25989994 - Br J Nutr. 2015 May 14;113(9):1339-44 24671237 - Eur J Nutr. 2015 Feb;54(1):89-99 20157338 - Nat Rev Microbiol. 2010 Mar;8(3):171-84 21297998 - PLoS One. 2011 Jan 27;6(1):e16393 24925303 - Br J Nutr. 2014 Aug 28;112(4):536-46 24059313 - CNS Neurol Disord Drug Targets. 2014 Mar;13(2):305-11 25302927 - J Am Coll Nutr. 2014;33(5):385-93 |
References_xml | – volume: 3 start-page: 36 year: 2015 ident: bib1150 article-title: Structure and function of the healthy pre-adolescent pediatric gut microbiome publication-title: Microbiome – volume: 37 start-page: 65 year: 2015 end-page: 72 ident: bib0955 article-title: Microbiome and cancer publication-title: Semin. Immunopathol. – volume: 6 start-page: e17447 year: 2011 ident: bib1155 article-title: Metatranscriptomic approach to analyze the functional human gut microbiota publication-title: PLoS ONE – volume: 8 start-page: e73140 year: 2013 ident: bib0860 article-title: Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon publication-title: PLoS ONE – volume: 108 start-page: 36 year: 2015 end-page: 44 ident: bib1230 article-title: Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model publication-title: J. Microbiol. Methods – volume: 75 start-page: 7537 year: 2009 end-page: 7541 ident: bib0785 article-title: Introducing mothur: open-source, platform-Independent, community-supported software for describing and comparing microbial communities publication-title: Appl. Environ. Microbiol. – volume: 112 start-page: 11941 year: 2015 end-page: 11946 ident: bib1125 article-title: Gut DNA viromes of Malawian twins discordant for severe acute malnutrition publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 15 start-page: 382 year: 2014 end-page: 392 ident: bib0695 article-title: The treatment-naïve microbiome in new-onset Crohn's disease publication-title: Cell Host Microbe – volume: 7 start-page: e34242 year: 2012 ident: bib1110 article-title: A core human microbiome as viewed through 16S rRNA sequence clusters publication-title: PLoS ONE – volume: 13 start-page: 581 year: 2016 end-page: 583 ident: bib0800 article-title: DADA2: high-resolution sample inference from Illumina amplicon data publication-title: Nat. Methods – volume: 113 start-page: 1339 year: 2015 end-page: 1344 ident: bib1315 article-title: Oligosaccharides in infant formula: more evidence to validate the role of prebiotics publication-title: Br. J. Nutr. – volume: 11 start-page: e0148698 year: 2016 ident: bib1115 article-title: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies publication-title: PLoS ONE – volume: 474 start-page: 327 year: 2011 end-page: 336 ident: bib0980 article-title: Human nutrition, the gut microbiome and the immune system publication-title: Nature – volume: 142 start-page: 23 year: 2015 end-page: 32 ident: bib0995 article-title: Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid publication-title: Indian J. Med. Res. – volume: 1 start-page: 6ra14 year: 2009 ident: bib1200 article-title: The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice publication-title: Sci. Transl. Med. – volume: 87 start-page: 41 year: 2014 end-page: 51 ident: bib0910 article-title: Impact of galacto-oligosaccharides on the gut microbiota composition and metabolic activity upon antibiotic treatment during in vitro fermentation publication-title: FEMS Microbiol. Ecol. – volume: 43 start-page: 65 year: 2014 end-page: 91 ident: bib1250 article-title: Microfluidics expanding the frontiers of microbial ecology publication-title: Annu. Rev. Biophys. – start-page: 115 year: 1975 end-page: 141 ident: bib0875 article-title: New human tumor cell lines publication-title: Human Tumor Cells In Vitro – volume: 49 start-page: 495 year: 2004 end-page: 507 ident: bib1225 article-title: PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem publication-title: FEMS Microbiol. Ecol. – volume: 9 start-page: 68 year: 2015 end-page: 80 ident: bib0795 article-title: Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution publication-title: ISME J. – volume: 64 start-page: 651 year: 1998 end-page: 658 ident: bib1080 article-title: Identification of bacterial isolates obtained from intestinal contents associated with 12,000-year-old mastodon remains publication-title: Appl. Environ. Microbiol. – volume: 10 start-page: e0125448 year: 2015 ident: bib1340 article-title: Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes publication-title: PLoS ONE – volume: 54 start-page: 89 year: 2015 end-page: 99 ident: bib0900 article-title: Prebiotic effect during the first year of life in healthy infants fed formula containing GOS as the only prebiotic: a multicentre, randomised, double-blind and placebo-controlled trial publication-title: Eur. J. Nutr. – volume: 13 start-page: 217 year: 2014 end-page: 223 ident: bib0755 article-title: The gut microbiome. Inflamm publication-title: Allergy Drug Targets – volume: 10 start-page: 607 year: 2012 end-page: 617 ident: bib0925 article-title: Going viral: next generation sequencing applied to human gut phage populations publication-title: Nat. Rev. Microbiol. – volume: 29 start-page: 621 year: 2013 end-page: 627 ident: bib0715 article-title: Molecular signatures for the dynamic process of establishing intestinal host-microbial homeostasis: potential for disease diagnostics? publication-title: Curr. Opin. Gastroenterol. – volume: 294 start-page: 115 year: 2004 end-page: 121 ident: bib0930 article-title: Shiga toxin-encoding bacteriophages–genomes in motion publication-title: Int. J. Med. Microbiol. – volume: 20 start-page: 1411 year: 2010 end-page: 1419 ident: bib0935 article-title: Reshaping the gut microbiome with bacterial transplantation and antibiotic intake publication-title: Genome Res. – volume: 111 start-page: E2329 year: 2014 end-page: E2338 ident: bib1160 article-title: Relating the metatranscriptome and metagenome of the human gut publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 114 start-page: 1132 year: 2013 end-page: 1146 ident: bib1310 article-title: Selective carbohydrate utilization by lactobacilli and bifidobacteria publication-title: J. Appl. Microbiol. – volume: 6 start-page: 161 year: 2015 end-page: 172 ident: bib0850 article-title: Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain publication-title: Gut Microbes. – volume: 98 start-page: F298 year: 2013 end-page: F303 ident: bib1065 article-title: Bacterial and fungal viability in the preterm gut: NEC and sepsis publication-title: Arch. Dis. Child. Fetal Neonatal. Ed. – volume: 10 start-page: e0138135 year: 2015 ident: bib1090 article-title: Gut microbiome of an 11th century A.D. Pre-Columbian Andean mummy publication-title: PLoS ONE – volume: 111 start-page: E2875 year: 2014 end-page: E2884 ident: bib0810 article-title: Oligotyping analysis of the human oral microbiome publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 113 start-page: E7 year: 2016 end-page: E15 ident: bib0885 article-title: Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 76 start-page: 2445 year: 2010 end-page: 2450 ident: bib1205 article-title: Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species publication-title: Appl. Environ. Microbiol. – volume: 68 start-page: 3878 year: 2002 end-page: 3885 ident: bib0740 article-title: High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates publication-title: Appl. Environ. Microbiol. – volume: 7 start-page: e30126 year: 2012 ident: bib0815 article-title: Dirichlet multinomial mixtures: generative models for microbial metagenomics publication-title: PLoS ONE – volume: 13 start-page: S7 year: 2014 ident: bib0770 article-title: Towards a better understanding of publication-title: Microb. Cell Fact. – volume: 11 start-page: 2577 year: 2005 end-page: 2591 ident: bib0730 article-title: Application of MALDI-TOF mass spectrometry in screening and diagnostic research publication-title: Curr. Pharm. Des. – volume: 11 start-page: e0147210 year: 2016 ident: bib0965 article-title: Changes in colonic bile acid composition following fecal microbiota transplantation are sufficient to control publication-title: PLoS ONE – year: 2013 ident: bib0805 article-title: Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data publication-title: Methods Ecol. Evol. – volume: 146 start-page: 1573 year: 2014 end-page: 1582 ident: bib0745 article-title: From stool transplants to next-generation microbiota therapeutics publication-title: Gastroenterology – volume: 8 start-page: 171 year: 2010 end-page: 184 ident: bib1335 article-title: Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens publication-title: Nat. Rev. Microbiol. – volume: 6 start-page: e16393 year: 2011 ident: bib0985 article-title: Microbial dysbiosis in colorectal cancer (CRC) patients publication-title: PLoS ONE – volume: 486 start-page: 215 year: 2012 end-page: 221 ident: bib1100 article-title: A framework for human microbiome research publication-title: Nature – volume: 33 start-page: 385 year: 2014 end-page: 393 ident: bib0905 article-title: Prebiotic effect of an infant formula supplemented with galacto-oligosaccharides: randomized multicenter trial publication-title: J. Am. Coll. Nutr. – volume: 489 start-page: 242 year: 2012 end-page: 249 ident: bib0685 article-title: Functional interactions between the gut microbiota and host metabolism publication-title: Nature – volume: 22 start-page: 320 year: 2015 end-page: 331 ident: bib1280 article-title: Quantifying diet-induced metabolic changes of the human gut microbiome publication-title: Cell Metab. – volume: 108 start-page: 6252 year: 2011 end-page: 6257 ident: bib1185 article-title: Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 9 start-page: 811 year: 2012 end-page: 814 ident: bib0825 article-title: Metagenomic microbial community profiling using unique clade-specific marker genes publication-title: Nat. Methods – volume: 70 start-page: 45 year: 2012 end-page: 56 ident: bib0975 article-title: Role of the intestinal microbiome in health and disease: from correlation to causation publication-title: Nutr. Rev. – volume: 2 start-page: 234 year: 2011 end-page: 243 ident: bib1055 article-title: Acute necrotizing enterocolitis of preterm piglets is characterized by dysbiosis of ileal mucosa-associated bacteria publication-title: Gut Microbes – volume: 12 start-page: 391 year: 2011 end-page: 403 ident: bib0735 article-title: Microbial metabolomics publication-title: Curr. Genomics – volume: 80 start-page: 9 year: 2014 end-page: 18 ident: bib1015 article-title: Genomic overview and biological functions of exopolysaccharide biosynthesis in publication-title: Appl. Environ. Microbiol. – volume: 12 start-page: 6119 year: 2015 end-page: 6127 ident: bib1325 article-title: Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer publication-title: Mol. Med. Rep. – volume: 31 start-page: 1231 year: 1987 end-page: 1233 ident: bib0915 article-title: Antimicrobial substance from a human publication-title: Antimicrob. Agents Chemother. – volume: 340 start-page: 1190 year: 2013 end-page: 1194 ident: bib0865 article-title: Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications publication-title: Science – volume: 110 start-page: 167 year: 2014 end-page: 176 ident: bib0760 article-title: The developing intestinal microbiome: probiotics and prebiotics publication-title: World Rev. Nutr. Diet. – volume: 26 start-page: 26191 year: 2015 ident: bib0990 article-title: Dysbiosis of the gut microbiota in disease publication-title: Microb. Ecol. Health Dis. – volume: 2 start-page: e593 year: 2014 ident: bib0790 article-title: Swarm: robust and fast clustering method for amplicon-based studies publication-title: PeerJ – volume: 8 start-page: 2135 year: 2013 end-page: 2157 ident: bib0870 article-title: Microfabrication of human organs-on-chips publication-title: Nat. Protoc. – volume: 13 start-page: 305 year: 2014 end-page: 311 ident: bib1025 article-title: Role of gut microbiota in obesity, type 2 diabetes and Alzheimer's disease publication-title: CNS Neurol. Disord. Drug Targets – volume: 31 start-page: 814 year: 2013 end-page: 821 ident: bib0830 article-title: Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences publication-title: Nat. Biotechnol. – volume: 108 start-page: 749 year: 1961 end-page: 752 ident: bib1050 article-title: Interactions of the oral microbiota. I. A system for the defined study of mixed cultures publication-title: Proc. Soc. Exp. Biol. Med. – volume: 9 start-page: 519 year: 2016 end-page: 524 ident: bib0700 article-title: Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted Qpcr publication-title: Microb. Biotechnol. – volume: 54 start-page: 249 year: 2003 end-page: 256 ident: bib1060 article-title: Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients publication-title: J. Microbiol. Methods – volume: 159 start-page: 227 year: 2014 end-page: 230 ident: bib1035 article-title: Advancing the microbiome research community publication-title: Cell – volume: 141 start-page: 513 year: 1995 end-page: 521 ident: bib1070 article-title: Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis publication-title: Microbiology – volume: 39 start-page: 198 year: 2015 end-page: 203 ident: bib0950 article-title: Gut microbiota and metabolic disorders publication-title: Diabetes Metab. J. – volume: 4 start-page: 1094 year: 2010 end-page: 1098 ident: bib1190 article-title: Creating and characterizing communities of human gut microbes in gnotobiotic mice publication-title: ISME J. – year: 2015 ident: bib1135 article-title: Gut inflammation and immunity: what is the role of the human gut virome? publication-title: Mediators Inflamm. – volume: 6 start-page: 220ra11 year: 2014 ident: bib1195 article-title: Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice publication-title: Sci. Transl. Med. – volume: 5 start-page: 1130 year: 2013 end-page: 1140 ident: bib0880 article-title: Gut-on-a-Chip microenvironment induces human intestinal cells to undergo villus differentiation publication-title: Integr. Biol. (Camb) – year: 2014 ident: bib0780 article-title: Fecal microbiota transplantation via colonoscopy for recurrent publication-title: J. Vis. Exp. – volume: 68 start-page: 51 year: 1956 end-page: 55 ident: bib1085 article-title: The effect of an antibiotic on the susceptibility of the mouse's intestinal tract to publication-title: Trans. Am. Clin. Climatol. Assoc – volume: 34 start-page: 39 year: 2013 end-page: 58 ident: bib1020 article-title: The gut microbiota, obesity and insulin resistance publication-title: Mol. Aspects Med. – volume: 150 start-page: 531 year: 2007 end-page: 538 ident: bib1005 article-title: Differential immunomodulatory properties of publication-title: Clin. Exp. Immunol. – volume: 83 start-page: 138 year: 2015 end-page: 145 ident: bib0895 article-title: Persistence and toxin production by publication-title: Infect. Immun. – volume: 20 start-page: 769 year: 2014 end-page: 778 ident: bib1300 article-title: Vitamin B12 as a modulator of gut microbial ecology publication-title: Cell Metab. – year: 2016 ident: bib1175 article-title: Benefits of short-chain fatty acids and their receptors in inflammation and carcinogenesis publication-title: Pharmacol. Ther. – volume: 505 start-page: 559 year: 2014 end-page: 563 ident: bib1270 article-title: Diet rapidly and reproducibly alters the human gut microbiome publication-title: Nature – volume: 42 start-page: 166 year: 2006 end-page: 170 ident: bib0920 article-title: Effect of maternal consumption of publication-title: J. Pediatr. Gastroenterol. Nutr. – volume: 12 start-page: 303 year: 2015 end-page: 310 ident: bib0960 article-title: Towards a more comprehensive concept for prebiotics publication-title: Nat. Rev. Gastroenterol. Hepatol. – volume: 38 start-page: 13 year: 2011 end-page: 20 ident: bib1120 article-title: Fungal microbiota from rain water and pathogenicity of publication-title: J. Ind. Microbiol. Biotechnol. – volume: 26 start-page: 28177 year: 2015 ident: bib0725 article-title: Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders publication-title: Microb. Ecol. Health Dis. – volume: 27 start-page: 701 year: 2013 end-page: 718 ident: bib1240 article-title: Exploring host-microbiota interactions in animal models and humans publication-title: Genes Dev. – volume: 68 start-page: 334 year: 2016 end-page: 340 ident: bib0970 article-title: Carrier systems for bacteriophages to supplement food systems: encapsulation and controlled release to modulate the human gut microbiota publication-title: LTW–Food Sci. Technol. – volume: 9 start-page: 3653 year: 2015 end-page: 3663 ident: bib1350 article-title: Bacteriophage-based therapy in cystic fibrosis-associated publication-title: Drug Des. Devel. Ther. – volume: 16 start-page: 549 year: 2015 ident: bib1165 article-title: Transcriptome analysis of bacteriophage communities in periodontal health and disease publication-title: BMC Genomics – volume: 27 start-page: 373 year: 2015 end-page: 380 ident: bib0690 article-title: Influence and effect of the human microbiome in allergy and asthma publication-title: Curr. Opin. Rheumatol. – volume: 18 start-page: 515 year: 2015 end-page: 520 ident: bib1290 article-title: Influence of high-fat diet on gut microbiota: a driving force for chronic disease risk publication-title: Curr. Opin. Clin. Nutr. Metab. Care – volume: 1 start-page: 187 year: 2015 end-page: 196 ident: bib0775 article-title: Engineering modular viral scaffolds for targeted bacterial population editing publication-title: Cell Systems – volume: 308 start-page: 1635 year: 2005 end-page: 1638 ident: bib1040 article-title: Diversity of the human intestinal microbial flora publication-title: Science – volume: 4 start-page: e005047 year: 2014 ident: bib0765 article-title: Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review publication-title: BMJ Open – volume: 9 start-page: 365 year: 1964 end-page: 370 ident: bib1045 article-title: Studies of the predominant cultivable microbiota of dental plaque publication-title: Arch. Oral Biol. – volume: 24 start-page: 1504 year: 2014 end-page: 1516 ident: bib1170 article-title: Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape publication-title: Genome Res. – volume: 32 start-page: 473 year: 2014 end-page: 478 ident: bib1215 article-title: Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption publication-title: Nat. Biotechnol. – volume: 65 start-page: 57 year: 2016 end-page: 62 ident: bib0820 article-title: Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates publication-title: Gut – volume: 8 start-page: 310 year: 2008 ident: bib1010 article-title: Anti-proliferative effects of publication-title: BMC Cancer – volume: 31 start-page: 107 year: 1977 end-page: 133 ident: bib0680 article-title: Microbial ecology of the gastrointestinal tract publication-title: Annu. Rev. Microbiol. – volume: 20 start-page: 731 year: 2014 end-page: 741 ident: bib0840 article-title: Determining microbial products and identifying molecular targets in the human microbiome publication-title: Cell Metab. – volume: 146 year: 2014 ident: bib0710 article-title: Meta’omic analytic techniques for studying the intestinal microbiome publication-title: Gastroenterology – volume: 4 start-page: 4 year: 2013 end-page: 16 ident: bib1140 article-title: Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota publication-title: Gut Microbes – volume: 83 start-page: 2926 year: 2015 end-page: 2934 ident: bib0890 article-title: Interaction of publication-title: Infect. Immun. – volume: 13 start-page: 390 year: 2015 end-page: 401 ident: bib0845 article-title: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome publication-title: Comput. Struct. Biotechnol. J. – year: 2016 ident: bib0705 article-title: Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability publication-title: Int. J. Med. Microbiol – volume: 10 start-page: e1001377 year: 2012 ident: bib0855 article-title: The Human Microbiome Project: a community resource for the healthy human microbiome publication-title: PLoS Biol. – volume: 24 start-page: 613 year: 2005 end-page: 646 ident: bib1180 article-title: Mass spectrometry in metabolome analysis publication-title: Mass Spectrom. Rev. – volume: 6 start-page: 206 year: 2015 end-page: 213 ident: bib0720 article-title: Microbial degradation of whole-grain complex carbohydrates and impact on short-chain fatty acids and health publication-title: Adv. Nutr. – volume: 27 start-page: 114 year: 2015 end-page: 120 ident: bib0750 article-title: Applications of imaging for bacterial systems biology publication-title: Curr. Opin. Microbiol. – volume: 486 start-page: 222 year: 2012 end-page: 227 ident: bib1295 article-title: Human gut microbiome viewed across age and geography publication-title: Nature – volume: 32 start-page: D277 year: 2004 end-page: D280 ident: bib1145 article-title: The KEGG resource for deciphering the genome publication-title: Nucleic Acids Res. – volume: 301 start-page: G401 year: 2011 end-page: G424 ident: bib1030 article-title: The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? publication-title: Am. J. Physiol. Gastrointest. Liver Physiol. – volume: 7 start-page: 247 year: 2016 end-page: 264 ident: bib1320 article-title: High purity galacto-oligosaccharides enhance specific publication-title: Benef. Microbes – volume: 7 start-page: 293ra103 year: 2015 ident: bib0940 article-title: Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis publication-title: Sci. Transl. Med. – volume: 466 start-page: 334 year: 2010 end-page: 338 ident: bib1130 article-title: Viruses in the fecal microbiota of monozygotic twins and their mothers publication-title: Nature – volume: 12 start-page: 2165 year: 2012 end-page: 2174 ident: bib1245 article-title: Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow publication-title: Lab Chip – volume: 56 start-page: 6235 year: 2012 end-page: 6242 ident: bib1345 article-title: Virulent bacteriophages can target O104:H4 enteroaggregative publication-title: Antimicrob. Agents Chemother. – volume: 112 start-page: 536 year: 2014 end-page: 546 ident: bib1305 article-title: Exploring the effects of galacto-oligosaccharides on the gut microbiota of healthy adults receiving amoxicillin treatment publication-title: Br. J. Nutr. – volume: 90 start-page: 417 year: 2014 end-page: 423 ident: bib1210 article-title: Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia publication-title: FEMS Microbiol. Ecol. – volume: 7 start-page: 335 year: 2010 end-page: 336 ident: bib1095 article-title: QIIME allows analysis of high-throughput community sequencing data publication-title: Nat. Methods – year: 2014 ident: bib1220 article-title: Survival and synergistic growth of mixed cultures of bifidobacteria and lactobacilli combined with prebiotic oligosaccharides in a gastrointestinal tract simulator publication-title: Microb. Ecol. Health Dis. – volume: 5 start-page: 106 year: 2015 ident: bib0945 article-title: serovar Typhimurium exploits inflammation to modify swine intestinal microbiota publication-title: Front. Cell. Infect. Microbiol. – volume: 5 start-page: 864 year: 2010 end-page: 872 ident: bib1255 article-title: Investigation of bacterial chemotaxis in flow-based microfluidic devices publication-title: Nat. Protoc. – volume: 18 start-page: 478 year: 2015 end-page: 488 ident: bib1235 article-title: Quantitative imaging of gut microbiota spatial organization publication-title: Cell Host Microbe. – volume: 17 start-page: 340 year: 2015 end-page: 349 ident: bib1265 article-title: A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis publication-title: Nat. Cell Biol. – volume: 87 start-page: S203 year: 2002 end-page: S211 ident: bib1075 article-title: Molecular biological methods for studying the gut microbiota: the EU human gut flora project publication-title: Br. J. Nutr. – volume: 11 start-page: 161 year: 2012 ident: bib1330 article-title: Lipoteichoic acid is an important microbe-associated molecular pattern of publication-title: Microb. Cell Fact. – volume: 7 start-page: e32118 year: 2012 ident: bib1105 article-title: Analyses of the microbial diversity across the human microbiome publication-title: PLoS ONE – volume: 8 start-page: e1002358 year: 2012 ident: bib0835 article-title: Metabolic reconstruction for metagenomic data and its application to the human microbiome publication-title: PLoS Comput Biol. – volume: 588 start-page: 4120 year: 2014 end-page: 4130 ident: bib1285 article-title: Beneficial modulation of the gut microbiota publication-title: FEBS Lett. – volume: 312 start-page: 1355 year: 2006 end-page: 1359 ident: bib1000 article-title: Metagenomic analysis of the human distal gut microbiome publication-title: Science – volume: 14 start-page: 1622 year: 2014 end-page: 1631 ident: bib1260 article-title: generation of colonic epithelium from primary cells guided by microstructures publication-title: Lab Chip – volume: 5 start-page: e12191 year: 2010 ident: bib1275 article-title: High-fat diet: bacteria interactions promote intestinal inflammation which precedes and correlates with obesity and insulin resistance in mouse publication-title: PLoS ONE – volume: 87 start-page: S203 issue: Suppl. 2 year: 2002 ident: 10.1016/j.tim.2016.06.008_bib1075 article-title: Molecular biological methods for studying the gut microbiota: the EU human gut flora project publication-title: Br. J. Nutr. doi: 10.1079/BJN/2002539 – volume: 7 start-page: e30126 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib0815 article-title: Dirichlet multinomial mixtures: generative models for microbial metagenomics publication-title: PLoS ONE doi: 10.1371/journal.pone.0030126 – volume: 112 start-page: 536 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1305 article-title: Exploring the effects of galacto-oligosaccharides on the gut microbiota of healthy adults receiving amoxicillin treatment publication-title: Br. J. Nutr. doi: 10.1017/S0007114514001135 – volume: 20 start-page: 769 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1300 article-title: Vitamin B12 as a modulator of gut microbial ecology publication-title: Cell Metab. doi: 10.1016/j.cmet.2014.10.002 – volume: 108 start-page: 749 year: 1961 ident: 10.1016/j.tim.2016.06.008_bib1050 article-title: Interactions of the oral microbiota. I. A system for the defined study of mixed cultures publication-title: Proc. Soc. Exp. Biol. Med. doi: 10.3181/00379727-108-27055 – volume: 68 start-page: 51 year: 1956 ident: 10.1016/j.tim.2016.06.008_bib1085 article-title: The effect of an antibiotic on the susceptibility of the mouse's intestinal tract to Salmonella infection publication-title: Trans. Am. Clin. Climatol. Assoc – volume: 111 start-page: E2875 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0810 article-title: Oligotyping analysis of the human oral microbiome publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1409644111 – volume: 26 start-page: 26191 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0990 article-title: Dysbiosis of the gut microbiota in disease publication-title: Microb. Ecol. Health Dis. – year: 2016 ident: 10.1016/j.tim.2016.06.008_bib0705 article-title: Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability publication-title: Int. J. Med. Microbiol doi: 10.1016/j.ijmm.2016.03.005 – volume: 4 start-page: 4 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib1140 article-title: Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota publication-title: Gut Microbes doi: 10.4161/gmic.22371 – volume: 142 start-page: 23 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0995 article-title: Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid publication-title: Indian J. Med. Res. doi: 10.4103/0971-5916.162091 – volume: 29 start-page: 621 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib0715 article-title: Molecular signatures for the dynamic process of establishing intestinal host-microbial homeostasis: potential for disease diagnostics? publication-title: Curr. Opin. Gastroenterol. doi: 10.1097/MOG.0b013e328365d365 – volume: 114 start-page: 1132 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib1310 article-title: Selective carbohydrate utilization by lactobacilli and bifidobacteria publication-title: J. Appl. Microbiol. doi: 10.1111/jam.12105 – volume: 2 start-page: e593 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0790 article-title: Swarm: robust and fast clustering method for amplicon-based studies publication-title: PeerJ doi: 10.7717/peerj.593 – year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1135 article-title: Gut inflammation and immunity: what is the role of the human gut virome? publication-title: Mediators Inflamm. doi: 10.1155/2015/326032 – volume: 2 start-page: 234 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib1055 article-title: Acute necrotizing enterocolitis of preterm piglets is characterized by dysbiosis of ileal mucosa-associated bacteria publication-title: Gut Microbes doi: 10.4161/gmic.2.4.16332 – volume: 42 start-page: 166 year: 2006 ident: 10.1016/j.tim.2016.06.008_bib0920 article-title: Effect of maternal consumption of Lactobacillus GG on transfer and establishment of fecal bifidobacterial microbiota in neonates publication-title: J. Pediatr. Gastroenterol. Nutr. doi: 10.1097/01.mpg.0000189346.25172.fd – volume: 38 start-page: 13 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib1120 article-title: Fungal microbiota from rain water and pathogenicity of Fusarium species isolated from atmospheric dust and rainfall dust publication-title: J. Ind. Microbiol. Biotechnol. doi: 10.1007/s10295-010-0831-5 – volume: 11 start-page: 2577 year: 2005 ident: 10.1016/j.tim.2016.06.008_bib0730 article-title: Application of MALDI-TOF mass spectrometry in screening and diagnostic research publication-title: Curr. Pharm. Des. doi: 10.2174/1381612054546932 – volume: 1 start-page: 6ra14 year: 2009 ident: 10.1016/j.tim.2016.06.008_bib1200 article-title: The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice publication-title: Sci. Transl. Med. doi: 10.1126/scitranslmed.3000322 – volume: 26 start-page: 28177 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0725 article-title: Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders publication-title: Microb. Ecol. Health Dis. – volume: 13 start-page: 217 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0755 article-title: The gut microbiome. Inflamm publication-title: Allergy Drug Targets doi: 10.2174/1871528113666140623113221 – volume: 11 start-page: e0147210 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib0965 article-title: Changes in colonic bile acid composition following fecal microbiota transplantation are sufficient to control Clostridium difficile germination and growth publication-title: PLoS ONE doi: 10.1371/journal.pone.0147210 – volume: 9 start-page: 365 year: 1964 ident: 10.1016/j.tim.2016.06.008_bib1045 article-title: Studies of the predominant cultivable microbiota of dental plaque publication-title: Arch. Oral Biol. doi: 10.1016/0003-9969(64)90069-X – volume: 489 start-page: 242 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib0685 article-title: Functional interactions between the gut microbiota and host metabolism publication-title: Nature doi: 10.1038/nature11552 – volume: 146 start-page: 1573 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0745 article-title: From stool transplants to next-generation microbiota therapeutics publication-title: Gastroenterology doi: 10.1053/j.gastro.2014.01.004 – volume: 16 start-page: 549 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1165 article-title: Transcriptome analysis of bacteriophage communities in periodontal health and disease publication-title: BMC Genomics doi: 10.1186/s12864-015-1781-0 – volume: 8 start-page: e73140 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib0860 article-title: Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon publication-title: PLoS ONE doi: 10.1371/journal.pone.0073140 – volume: 87 start-page: 41 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0910 article-title: Impact of galacto-oligosaccharides on the gut microbiota composition and metabolic activity upon antibiotic treatment during in vitro fermentation publication-title: FEMS Microbiol. Ecol. doi: 10.1111/1574-6941.12187 – volume: 31 start-page: 1231 year: 1987 ident: 10.1016/j.tim.2016.06.008_bib0915 article-title: Antimicrobial substance from a human Lactobacillus strain publication-title: Antimicrob. Agents Chemother. doi: 10.1128/AAC.31.8.1231 – volume: 6 start-page: 206 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0720 article-title: Microbial degradation of whole-grain complex carbohydrates and impact on short-chain fatty acids and health publication-title: Adv. Nutr. doi: 10.3945/an.114.007450 – volume: 5 start-page: 864 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib1255 article-title: Investigation of bacterial chemotaxis in flow-based microfluidic devices publication-title: Nat. Protoc. doi: 10.1038/nprot.2010.18 – volume: 9 start-page: 68 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0795 article-title: Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution publication-title: ISME J. doi: 10.1038/ismej.2014.117 – volume: 9 start-page: 519 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib0700 article-title: Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted Qpcr publication-title: Microb. Biotechnol. doi: 10.1111/1751-7915.12366 – volume: 6 start-page: 220ra11 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1195 article-title: Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice publication-title: Sci. Transl. Med. doi: 10.1126/scitranslmed.3008051 – volume: 4 start-page: e005047 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0765 article-title: Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review publication-title: BMJ Open doi: 10.1136/bmjopen-2014-005047 – volume: 5 start-page: 1130 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib0880 article-title: Gut-on-a-Chip microenvironment induces human intestinal cells to undergo villus differentiation publication-title: Integr. Biol. (Camb) doi: 10.1039/c3ib40126j – volume: 27 start-page: 373 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0690 article-title: Influence and effect of the human microbiome in allergy and asthma publication-title: Curr. Opin. Rheumatol. doi: 10.1097/BOR.0000000000000191 – volume: 12 start-page: 303 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0960 article-title: Towards a more comprehensive concept for prebiotics publication-title: Nat. Rev. Gastroenterol. Hepatol. doi: 10.1038/nrgastro.2015.47 – volume: 6 start-page: e17447 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib1155 article-title: Metatranscriptomic approach to analyze the functional human gut microbiota publication-title: PLoS ONE doi: 10.1371/journal.pone.0017447 – volume: 20 start-page: 731 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0840 article-title: Determining microbial products and identifying molecular targets in the human microbiome publication-title: Cell Metab. doi: 10.1016/j.cmet.2014.10.003 – volume: 113 start-page: 1339 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1315 article-title: Oligosaccharides in infant formula: more evidence to validate the role of prebiotics publication-title: Br. J. Nutr. doi: 10.1017/S0007114515000823 – volume: 76 start-page: 2445 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib1205 article-title: Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.01754-09 – volume: 80 start-page: 9 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1015 article-title: Genomic overview and biological functions of exopolysaccharide biosynthesis in Bifidobacterium spp publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.02977-13 – year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1220 article-title: Survival and synergistic growth of mixed cultures of bifidobacteria and lactobacilli combined with prebiotic oligosaccharides in a gastrointestinal tract simulator publication-title: Microb. Ecol. Health Dis. doi: 10.3402/mehd.v25.23062 – volume: 13 start-page: 390 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0845 article-title: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome publication-title: Comput. Struct. Biotechnol. J. doi: 10.1016/j.csbj.2015.06.001 – volume: 301 start-page: G401 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib1030 article-title: The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? publication-title: Am. J. Physiol. Gastrointest. Liver Physiol. doi: 10.1152/ajpgi.00110.2011 – volume: 32 start-page: D277 issue: Database issue year: 2004 ident: 10.1016/j.tim.2016.06.008_bib1145 article-title: The KEGG resource for deciphering the genome publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh063 – volume: 474 start-page: 327 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib0980 article-title: Human nutrition, the gut microbiome and the immune system publication-title: Nature doi: 10.1038/nature10213 – volume: 9 start-page: 3653 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1350 article-title: Bacteriophage-based therapy in cystic fibrosis-associated Pseudomonas aeruginosa infections: rationale and current status publication-title: Drug Des. Devel. Ther. – year: 2013 ident: 10.1016/j.tim.2016.06.008_bib0805 article-title: Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data publication-title: Methods Ecol. Evol. doi: 10.1111/2041-210X.12114 – volume: 141 start-page: 513 issue: Pt 2 year: 1995 ident: 10.1016/j.tim.2016.06.008_bib1070 article-title: Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis publication-title: Microbiology doi: 10.1099/13500872-141-2-513 – volume: 37 start-page: 65 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0955 article-title: Microbiome and cancer publication-title: Semin. Immunopathol. doi: 10.1007/s00281-014-0457-1 – volume: 49 start-page: 495 year: 2004 ident: 10.1016/j.tim.2016.06.008_bib1225 article-title: PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem publication-title: FEMS Microbiol. Ecol. doi: 10.1016/j.femsec.2004.05.002 – volume: 34 start-page: 39 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib1020 article-title: The gut microbiota, obesity and insulin resistance publication-title: Mol. Aspects Med. doi: 10.1016/j.mam.2012.11.001 – volume: 11 start-page: e0148698 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib1115 article-title: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies publication-title: PLoS ONE doi: 10.1371/journal.pone.0148698 – volume: 110 start-page: 167 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0760 article-title: The developing intestinal microbiome: probiotics and prebiotics publication-title: World Rev. Nutr. Diet. doi: 10.1159/000358465 – start-page: 115 year: 1975 ident: 10.1016/j.tim.2016.06.008_bib0875 article-title: New human tumor cell lines – volume: 54 start-page: 249 year: 2003 ident: 10.1016/j.tim.2016.06.008_bib1060 article-title: Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients publication-title: J. Microbiol. Methods doi: 10.1016/S0167-7012(03)00059-9 – volume: 308 start-page: 1635 year: 2005 ident: 10.1016/j.tim.2016.06.008_bib1040 article-title: Diversity of the human intestinal microbial flora publication-title: Science doi: 10.1126/science.1110591 – volume: 486 start-page: 222 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib1295 article-title: Human gut microbiome viewed across age and geography publication-title: Nature doi: 10.1038/nature11053 – volume: 340 start-page: 1190 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib0865 article-title: Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications publication-title: Science doi: 10.1126/science.1234852 – year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0780 article-title: Fecal microbiota transplantation via colonoscopy for recurrent C. difficile infection publication-title: J. Vis. Exp. doi: 10.3791/52154 – volume: 98 start-page: F298 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib1065 article-title: Bacterial and fungal viability in the preterm gut: NEC and sepsis publication-title: Arch. Dis. Child. Fetal Neonatal. Ed. doi: 10.1136/archdischild-2012-302119 – volume: 43 start-page: 65 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1250 article-title: Microfluidics expanding the frontiers of microbial ecology publication-title: Annu. Rev. Biophys. doi: 10.1146/annurev-biophys-051013-022916 – volume: 588 start-page: 4120 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1285 article-title: Beneficial modulation of the gut microbiota publication-title: FEBS Lett. doi: 10.1016/j.febslet.2014.03.035 – volume: 4 start-page: 1094 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib1190 article-title: Creating and characterizing communities of human gut microbes in gnotobiotic mice publication-title: ISME J. doi: 10.1038/ismej.2010.110 – volume: 10 start-page: 607 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib0925 article-title: Going viral: next generation sequencing applied to human gut phage populations publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro2853 – volume: 83 start-page: 138 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0895 article-title: Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function publication-title: Infect. Immun. doi: 10.1128/IAI.02561-14 – volume: 20 start-page: 1411 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib0935 article-title: Reshaping the gut microbiome with bacterial transplantation and antibiotic intake publication-title: Genome Res. doi: 10.1101/gr.107987.110 – volume: 70 start-page: 45 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib0975 article-title: Role of the intestinal microbiome in health and disease: from correlation to causation publication-title: Nutr. Rev. doi: 10.1111/j.1753-4887.2012.00505.x – volume: 13 start-page: S7 issue: Suppl. 1 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0770 article-title: Towards a better understanding of Lactobacillus rhamnosus GG–host interactions publication-title: Microb. Cell Fact. doi: 10.1186/1475-2859-13-S1-S7 – volume: 108 start-page: 6252 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib1185 article-title: Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1102938108 – volume: 18 start-page: 515 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1290 article-title: Influence of high-fat diet on gut microbiota: a driving force for chronic disease risk publication-title: Curr. Opin. Clin. Nutr. Metab. Care doi: 10.1097/MCO.0000000000000209 – year: 2016 ident: 10.1016/j.tim.2016.06.008_bib1175 article-title: Benefits of short-chain fatty acids and their receptors in inflammation and carcinogenesis publication-title: Pharmacol. Ther. doi: 10.1016/j.pharmthera.2016.04.007 – volume: 1 start-page: 187 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0775 article-title: Engineering modular viral scaffolds for targeted bacterial population editing publication-title: Cell Systems doi: 10.1016/j.cels.2015.08.013 – volume: 113 start-page: E7 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib0885 article-title: Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1522193112 – volume: 27 start-page: 114 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0750 article-title: Applications of imaging for bacterial systems biology publication-title: Curr. Opin. Microbiol. doi: 10.1016/j.mib.2015.08.003 – volume: 68 start-page: 3878 year: 2002 ident: 10.1016/j.tim.2016.06.008_bib0740 article-title: High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.68.8.3878-3885.2002 – volume: 90 start-page: 417 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1210 article-title: Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia publication-title: FEMS Microbiol. Ecol. – volume: 68 start-page: 334 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib0970 article-title: Carrier systems for bacteriophages to supplement food systems: encapsulation and controlled release to modulate the human gut microbiota publication-title: LTW–Food Sci. Technol. – volume: 24 start-page: 1504 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1170 article-title: Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape publication-title: Genome Res. doi: 10.1101/gr.165845.113 – volume: 12 start-page: 6119 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1325 article-title: Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer publication-title: Mol. Med. Rep. doi: 10.3892/mmr.2015.4124 – volume: 33 start-page: 385 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0905 article-title: Prebiotic effect of an infant formula supplemented with galacto-oligosaccharides: randomized multicenter trial publication-title: J. Am. Coll. Nutr. doi: 10.1080/07315724.2013.878232 – volume: 159 start-page: 227 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1035 article-title: Advancing the microbiome research community publication-title: Cell doi: 10.1016/j.cell.2014.09.022 – volume: 111 start-page: E2329 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1160 article-title: Relating the metatranscriptome and metagenome of the human gut publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1319284111 – volume: 5 start-page: 106 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0945 article-title: Salmonella enterica serovar Typhimurium exploits inflammation to modify swine intestinal microbiota publication-title: Front. Cell. Infect. Microbiol. – volume: 7 start-page: e32118 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib1105 article-title: Analyses of the microbial diversity across the human microbiome publication-title: PLoS ONE doi: 10.1371/journal.pone.0032118 – volume: 13 start-page: 581 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib0800 article-title: DADA2: high-resolution sample inference from Illumina amplicon data publication-title: Nat. Methods doi: 10.1038/nmeth.3869 – volume: 17 start-page: 340 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1265 article-title: A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis publication-title: Nat. Cell Biol. doi: 10.1038/ncb3104 – volume: 466 start-page: 334 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib1130 article-title: Viruses in the fecal microbiota of monozygotic twins and their mothers publication-title: Nature doi: 10.1038/nature09199 – volume: 75 start-page: 7537 year: 2009 ident: 10.1016/j.tim.2016.06.008_bib0785 article-title: Introducing mothur: open-source, platform-Independent, community-supported software for describing and comparing microbial communities publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.01541-09 – volume: 8 start-page: 310 year: 2008 ident: 10.1016/j.tim.2016.06.008_bib1010 article-title: Anti-proliferative effects of Bifidobacterium adolescentis SPM0212 extract on human colon cancer cell lines publication-title: BMC Cancer doi: 10.1186/1471-2407-8-310 – volume: 27 start-page: 701 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib1240 article-title: Exploring host-microbiota interactions in animal models and humans publication-title: Genes Dev. doi: 10.1101/gad.212522.112 – volume: 10 start-page: e1001377 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib0855 article-title: The Human Microbiome Project: a community resource for the healthy human microbiome publication-title: PLoS Biol. doi: 10.1371/journal.pbio.1001377 – volume: 312 start-page: 1355 year: 2006 ident: 10.1016/j.tim.2016.06.008_bib1000 article-title: Metagenomic analysis of the human distal gut microbiome publication-title: Science doi: 10.1126/science.1124234 – volume: 18 start-page: 478 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1235 article-title: Quantitative imaging of gut microbiota spatial organization publication-title: Cell Host Microbe. doi: 10.1016/j.chom.2015.09.002 – volume: 7 start-page: 335 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib1095 article-title: QIIME allows analysis of high-throughput community sequencing data publication-title: Nat. Methods doi: 10.1038/nmeth.f.303 – volume: 22 start-page: 320 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1280 article-title: Quantifying diet-induced metabolic changes of the human gut microbiome publication-title: Cell Metab. doi: 10.1016/j.cmet.2015.07.001 – volume: 65 start-page: 57 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib0820 article-title: Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates publication-title: Gut doi: 10.1136/gutjnl-2015-309618 – volume: 39 start-page: 198 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0950 article-title: Gut microbiota and metabolic disorders publication-title: Diabetes Metab. J. doi: 10.4093/dmj.2015.39.3.198 – volume: 56 start-page: 6235 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib1345 article-title: Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine publication-title: Antimicrob. Agents Chemother. doi: 10.1128/AAC.00602-12 – volume: 6 start-page: e16393 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib0985 article-title: Microbial dysbiosis in colorectal cancer (CRC) patients publication-title: PLoS ONE doi: 10.1371/journal.pone.0016393 – volume: 31 start-page: 814 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib0830 article-title: Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2676 – volume: 5 start-page: e12191 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib1275 article-title: High-fat diet: bacteria interactions promote intestinal inflammation which precedes and correlates with obesity and insulin resistance in mouse publication-title: PLoS ONE doi: 10.1371/journal.pone.0012191 – volume: 108 start-page: 36 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1230 article-title: Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model publication-title: J. Microbiol. Methods doi: 10.1016/j.mimet.2014.11.007 – volume: 12 start-page: 2165 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib1245 article-title: Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow publication-title: Lab Chip doi: 10.1039/c2lc40074j – volume: 24 start-page: 613 year: 2005 ident: 10.1016/j.tim.2016.06.008_bib1180 article-title: Mass spectrometry in metabolome analysis publication-title: Mass Spectrom. Rev. doi: 10.1002/mas.20032 – volume: 150 start-page: 531 year: 2007 ident: 10.1016/j.tim.2016.06.008_bib1005 article-title: Differential immunomodulatory properties of Bifidobacterium logum strains: relevance to probiotic selection and clinical applications publication-title: Clin. Exp. Immunol. doi: 10.1111/j.1365-2249.2007.03522.x – volume: 10 start-page: e0138135 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1090 article-title: Gut microbiome of an 11th century A.D. Pre-Columbian Andean mummy publication-title: PLoS ONE doi: 10.1371/journal.pone.0138135 – volume: 8 start-page: 171 year: 2010 ident: 10.1016/j.tim.2016.06.008_bib1335 article-title: Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro2297 – volume: 3 start-page: 36 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1150 article-title: Structure and function of the healthy pre-adolescent pediatric gut microbiome publication-title: Microbiome doi: 10.1186/s40168-015-0101-x – volume: 9 start-page: 811 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib0825 article-title: Metagenomic microbial community profiling using unique clade-specific marker genes publication-title: Nat. Methods doi: 10.1038/nmeth.2066 – volume: 83 start-page: 2926 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0890 article-title: Interaction of Salmonella enterica serovar Typhimurium with intestinal organoids derived from human induced pluripotent stem cells publication-title: Infect. Immun. doi: 10.1128/IAI.00161-15 – volume: 32 start-page: 473 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1215 article-title: Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2857 – volume: 505 start-page: 559 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1270 article-title: Diet rapidly and reproducibly alters the human gut microbiome publication-title: Nature doi: 10.1038/nature12820 – volume: 8 start-page: 2135 year: 2013 ident: 10.1016/j.tim.2016.06.008_bib0870 article-title: Microfabrication of human organs-on-chips publication-title: Nat. Protoc. doi: 10.1038/nprot.2013.137 – volume: 112 start-page: 11941 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1125 article-title: Gut DNA viromes of Malawian twins discordant for severe acute malnutrition publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1514285112 – volume: 11 start-page: 161 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib1330 article-title: Lipoteichoic acid is an important microbe-associated molecular pattern of Lactobacillus rhamnosus GG publication-title: Microb. Cell Fact. doi: 10.1186/1475-2859-11-161 – volume: 12 start-page: 391 year: 2011 ident: 10.1016/j.tim.2016.06.008_bib0735 article-title: Microbial metabolomics publication-title: Curr. Genomics doi: 10.2174/138920211797248619 – volume: 64 start-page: 651 year: 1998 ident: 10.1016/j.tim.2016.06.008_bib1080 article-title: Identification of bacterial isolates obtained from intestinal contents associated with 12,000-year-old mastodon remains publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.64.2.651-658.1998 – volume: 10 start-page: e0125448 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib1340 article-title: Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes publication-title: PLoS ONE doi: 10.1371/journal.pone.0125448 – volume: 6 start-page: 161 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0850 article-title: Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain publication-title: Gut Microbes. doi: 10.1080/19490976.2015.1039223 – volume: 7 start-page: 293ra103 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0940 article-title: Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis publication-title: Sci. Transl. Med. doi: 10.1126/scitranslmed.aab2009 – volume: 14 start-page: 1622 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1260 article-title: In vitro generation of colonic epithelium from primary cells guided by microstructures publication-title: Lab Chip doi: 10.1039/C3LC51353J – volume: 294 start-page: 115 year: 2004 ident: 10.1016/j.tim.2016.06.008_bib0930 article-title: Shiga toxin-encoding bacteriophages–genomes in motion publication-title: Int. J. Med. Microbiol. doi: 10.1016/j.ijmm.2004.06.023 – volume: 146 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0710 article-title: Meta’omic analytic techniques for studying the intestinal microbiome publication-title: Gastroenterology doi: 10.1053/j.gastro.2014.01.049 – volume: 54 start-page: 89 year: 2015 ident: 10.1016/j.tim.2016.06.008_bib0900 article-title: Prebiotic effect during the first year of life in healthy infants fed formula containing GOS as the only prebiotic: a multicentre, randomised, double-blind and placebo-controlled trial publication-title: Eur. J. Nutr. doi: 10.1007/s00394-014-0689-9 – volume: 8 start-page: e1002358 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib0835 article-title: Metabolic reconstruction for metagenomic data and its application to the human microbiome publication-title: PLoS Comput Biol. doi: 10.1371/journal.pcbi.1002358 – volume: 31 start-page: 107 year: 1977 ident: 10.1016/j.tim.2016.06.008_bib0680 article-title: Microbial ecology of the gastrointestinal tract publication-title: Annu. Rev. Microbiol. doi: 10.1146/annurev.mi.31.100177.000543 – volume: 7 start-page: 247 year: 2016 ident: 10.1016/j.tim.2016.06.008_bib1320 article-title: High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome publication-title: Benef. Microbes doi: 10.3920/BM2015.0114 – volume: 15 start-page: 382 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib0695 article-title: The treatment-naïve microbiome in new-onset Crohn's disease publication-title: Cell Host Microbe doi: 10.1016/j.chom.2014.02.005 – volume: 13 start-page: 305 year: 2014 ident: 10.1016/j.tim.2016.06.008_bib1025 article-title: Role of gut microbiota in obesity, type 2 diabetes and Alzheimer's disease publication-title: CNS Neurol. Disord. Drug Targets doi: 10.2174/18715273113126660147 – volume: 7 start-page: e34242 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib1110 article-title: A core human microbiome as viewed through 16S rRNA sequence clusters publication-title: PLoS ONE doi: 10.1371/journal.pone.0034242 – volume: 486 start-page: 215 year: 2012 ident: 10.1016/j.tim.2016.06.008_bib1100 article-title: A framework for human microbiome research publication-title: Nature doi: 10.1038/nature11209 – reference: 20157338 - Nat Rev Microbiol. 2010 Mar;8(3):171-84 – reference: 23592793 - Genes Dev. 2013 Apr 1;27(7):701-18 – reference: 26261163 - Indian J Med Res. 2015 Jul;142(1):23-32 – reference: 25012900 - ISME J. 2015 Jan;9(1):68-80 – reference: 25078251 - FEMS Microbiol Ecol. 2014 Nov;90(2):417-23 – reference: 24705516 - Nat Biotechnol. 2014 May;32(5):473-8 – reference: 21677749 - Nature. 2011 Jun 15;474(7351):327-36 – reference: 22719823 - PLoS One. 2012;7(6):e32118 – reference: 26031685 - Microb Ecol Health Dis. 2015 May 29;26:28177 – reference: 26439864 - Cell Host Microbe. 2015 Oct 14;18(4):478-88 – reference: 20820862 - J Ind Microbiol Biotechnol. 2011 Jan;38(1):13-20 – reference: 25045346 - Microb Ecol Health Dis. 2014 Jul 15;25:null – reference: 15493821 - Int J Med Microbiol. 2004 Sep;294(2-3):115-21 – reference: 26002029 - Curr Opin Rheumatol. 2015 Jul;27(4):373-80 – reference: 15389842 - Mass Spectrom Rev. 2005 Sep-Oct;24(5):613-46 – reference: 25989994 - Br J Nutr. 2015 May 14;113(9):1339-44 – reference: 25770259 - Adv Nutr. 2015 Mar 13;6(2):206-13 – reference: 27113407 - Pharmacol Ther. 2016 Aug;164:144-51 – reference: 25549239 - J Vis Exp. 2014 Dec 08;(94):null – reference: 22699610 - Nature. 2012 Jun 13;486(7402):215-21 – reference: 23744940 - Science. 2013 Jun 7;340(6137):1190-4 – reference: 23022738 - Gut Microbes. 2013 Jan-Feb;4(1):4-16 – reference: 25970503 - PLoS One. 2015 May 13;10(5):e0125448 – reference: 24015295 - PLoS One. 2013 Aug 27;8(8):e73140 – reference: 22688413 - Nat Methods. 2012 Jun 10;9(8):811-4 – reference: 22699611 - Nature. 2012 May 09;486(7402):222-7 – reference: 25276506 - PeerJ. 2014 Sep 25;2:e593 – reference: 26238090 - Mol Med Rep. 2015 Oct;12(4):6119-27 – reference: 22319561 - PLoS One. 2012;7(2):e30126 – reference: 24113786 - Nat Protoc. 2013 Nov;8(11):2135-57 – reference: 24100720 - Curr Opin Gastroenterol. 2013 Nov;29(6):621-7 – reference: 26351661 - Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11941-6 – reference: 25186587 - Microb Cell Fact. 2014 Aug 29;13 Suppl 1:S7 – reference: 25440055 - Cell Metab. 2014 Nov 4;20(5):731-41 – reference: 20173072 - Appl Environ Microbiol. 2010 Apr;76(8):2445-50 – reference: 14483927 - Proc Soc Exp Biol Med. 1961 Dec;108:749-52 – reference: 21983069 - Gut Microbes. 2011 Jul-Aug;2(4):234-43 – reference: 25651997 - Microb Ecol Health Dis. 2015 Feb 02;26:26191 – reference: 24647645 - Lab Chip. 2014 May 7;14(9):1622-31 – reference: 24059313 - CNS Neurol Disord Drug Targets. 2014 Mar;13(2):305-11 – reference: 24965363 - Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):E2875-84 – reference: 26244934 - Cell Metab. 2015 Aug 4;22(2):320-31 – reference: 22864264 - Nat Rev Microbiol. 2012 Sep;10(9):607-17 – reference: 24925303 - Br J Nutr. 2014 Aug 28;112(4):536-46 – reference: 21436049 - Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6252-7 – reference: 26356259 - Curr Opin Microbiol. 2015 Oct;27:114-20 – reference: 24671237 - Eur J Nutr. 2015 Feb;54(1):89-99 – reference: 20368178 - Sci Transl Med. 2009 Nov 11;1(6):6ra14 – reference: 16741115 - Science. 2006 Jun 2;312(5778):1355-9 – reference: 25404117 - Semin Immunopathol. 2015 Jan;37(1):65-72 – reference: 24963153 - Genome Res. 2014 Sep;24(9):1504-16 – reference: 24412527 - Gastroenterology. 2014 May;146(6):1573-82 – reference: 26973885 - Cell Syst. 2015 Sep 23;1(3):187-196 – reference: 26215258 - BMC Genomics. 2015 Jul 28;16:549 – reference: 26839072 - Benef Microbes. 2016;7(2):247-64 – reference: 23240984 - J Appl Microbiol. 2013 Apr;114(4):1132-46 – reference: 24843156 - Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38 – reference: 26124989 - Diabetes Metab J. 2015 Jun;39(3):198-203 – reference: 20431532 - Nat Protoc. 2010 May;5(5):864-72 – reference: 24336217 - Nature. 2014 Jan 23;505(7484):559-63 – reference: 22861807 - Nutr Rev. 2012 Aug;70 Suppl 1:S45-56 – reference: 21700901 - Am J Physiol Gastrointest Liver Physiol. 2011 Sep;301(3):G401-24 – reference: 24123746 - Appl Environ Microbiol. 2014 Jan;80(1):9-18 – reference: 23975157 - Nat Biotechnol. 2013 Sep;31(9):814-21 – reference: 23426613 - Arch Dis Child Fetal Neonatal Ed. 2013 Jul;98(4):F298-303 – reference: 24629344 - Cell Host Microbe. 2014 Mar 12;15(3):382-92 – reference: 15831718 - Science. 2005 Jun 10;308(5728):1635-8 – reference: 26950069 - PLoS One. 2016 Mar 07;11(3):e0148698 – reference: 25302927 - J Am Coll Nutr. 2014;33(5):385-93 – reference: 22719824 - PLoS One. 2012;7(6):e34242 – reference: 22972297 - Nature. 2012 Sep 13;489(7415):242-9 – reference: 26306392 - Microbiome. 2015 Aug 26;3:36 – reference: 12088520 - Br J Nutr. 2002 May;87 Suppl 2:S203-11 – reference: 20808947 - PLoS One. 2010 Aug 16;5(8):e12191 – reference: 26668389 - Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):E7-15 – reference: 24751628 - World Rev Nutr Diet. 2014;110:167-76 – reference: 26213462 - Drug Des Devel Ther. 2015 Jul 16;9:3653-63 – reference: 19712298 - FEMS Microbiol Ecol. 2004 Sep 1;49(3):495-507 – reference: 25303518 - Cell. 2014 Oct 9;159(2):227-30 – reference: 26154278 - Curr Opin Clin Nutr Metab Care. 2015 Sep;18(5):515-20 – reference: 21408168 - PLoS One. 2011 Mar 08;6(3):e17447 – reference: 25964470 - Infect Immun. 2015 Jul;83(7):2926-34 – reference: 17956582 - Clin Exp Immunol. 2007 Dec;150(3):531-8 – reference: 26137199 - Comput Struct Biotechnol J. 2015 Jun 09;13:390-401 – reference: 25824997 - Nat Rev Gastroenterol Hepatol. 2015 May;12(5):303-10 – reference: 25157183 - BMJ Open. 2014 Aug 25;4(8):e005047 – reference: 16101460 - Curr Pharm Des. 2005;11(20):2577-91 – reference: 23159341 - Mol Aspects Med. 2013 Feb;34(1):39-58 – reference: 23241240 - Microb Cell Fact. 2012 Dec 15;11:161 – reference: 26835435 - Front Cell Infect Microbiol. 2016 Jan 22;5:106 – reference: 24953716 - Inflamm Allergy Drug Targets. 2014;13(4):217-23 – reference: 14170653 - Arch Oral Biol. 1964 May-Jun;9:365-70 – reference: 16456409 - J Pediatr Gastroenterol Nutr. 2006 Feb;42(2):166-70 – reference: 25440056 - Cell Metab. 2014 Nov 4;20(5):769-78 – reference: 7704280 - Microbiology. 1995 Feb;141 ( Pt 2):513-21 – reference: 24486053 - Gastroenterology. 2014 May;146(6):1437-1448.e1 – reference: 19801464 - Appl Environ Microbiol. 2009 Dec;75(23):7537-41 – reference: 334036 - Annu Rev Microbiol. 1977;31:107-33 – reference: 24452263 - Sci Transl Med. 2014 Jan 22;6(220):220ra11 – reference: 21297998 - PLoS One. 2011 Jan 27;6(1):e16393 – reference: 25875428 - Gut Microbes. 2015;6(3):161-72 – reference: 23909489 - FEMS Microbiol Ecol. 2014 Jan;87(1):41-51 – reference: 24681100 - FEBS Lett. 2014 Nov 17;588(22):4120-30 – reference: 26109103 - Sci Transl Med. 2015 Jun 24;7(293):293ra103 – reference: 26069274 - Gut. 2016 Jan;65(1):57-62 – reference: 18950540 - BMC Cancer. 2008 Oct 27;8:310 – reference: 26422376 - PLoS One. 2015 Sep 30;10(9):e0138135 – reference: 22379393 - Curr Genomics. 2011 Sep;12(6):391-403 – reference: 22719234 - PLoS Comput Biol. 2012;8(6):e1002358 – reference: 22904687 - PLoS Biol. 2012;10(8):e1001377 – reference: 23006754 - Antimicrob Agents Chemother. 2012 Dec;56(12):6235-42 – reference: 24358444 - Methods Ecol Evol. 2013 Dec 1;4(12):null – reference: 25664616 - Nat Cell Biol. 2015 Mar;17(3):340-9 – reference: 14681412 - Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80 – reference: 20383131 - Nat Methods. 2010 May;7(5):335-6 – reference: 20736229 - Genome Res. 2010 Oct;20(10):1411-9 – reference: 25462016 - J Microbiol Methods. 2015 Jan;108:36-44 – reference: 9464403 - Appl Environ Microbiol. 1998 Feb;64(2):651-8 – reference: 27214047 - Nat Methods. 2016 Jul;13(7):581-3 – reference: 26789728 - PLoS One. 2016 Jan 20;11(1):e0147210 – reference: 13486607 - Trans Am Clin Climatol Assoc. 1956-1957;68:51-5; discussion 55-8 – reference: 23817533 - Integr Biol (Camb). 2013 Sep;5(9):1130-40 – reference: 22434367 - Lab Chip. 2012 Jun 21;12(12):2165-74 – reference: 12147485 - Appl Environ Microbiol. 2002 Aug;68(8):3878-85 – reference: 25312952 - Infect Immun. 2015 Jan;83(1):138-45 – reference: 12782380 - J Microbiol Methods. 2003 Aug;54(2):249-56 – reference: 25944980 - Mediators Inflamm. 2015;2015:326032 – reference: 27052158 - Int J Med Microbiol. 2016 Aug;306(5):334-42 – reference: 20664551 - ISME J. 2010 Sep;4(9):1094-8 – reference: 20631792 - Nature. 2010 Jul 15;466(7304):334-8 – reference: 27166579 - Microb Biotechnol. 2016 Jul;9(4):519-24 – reference: 24773019 - Annu Rev Biophys. 2014;43:65-91 – reference: 3307619 - Antimicrob Agents Chemother. 1987 Aug;31(8):1231-3 |
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