Dynamics of the gut microbiome in subjects challenged with Shigella sonnei 53G in a controlled human infection model

Diarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to entero...

Full description

Saved in:
Bibliographic Details
Published inmSphere Vol. 10; no. 4; p. e0090624
Main Authors Liechty, Zachary, Baldwin, Arianna, Isidean, Sandra, Suvarnapunya, Akamol, Frenck, Robert, Porter, Chad, Goodson, Michael
Format Journal Article
LanguageEnglish
Published United States American Society for Microbiology 29.04.2025
Subjects
16S rRNA
Adult
Anti-Bacterial Agents - therapeutic use
Bacteria - classification
Bacteria - genetics
Bacteria - isolation & purification
controlled human infection model
diarrhea
Dysentery, Bacillary - drug therapy
Dysentery, Bacillary - microbiology
fecal microbiome
Feces - microbiology
Female
Gastrointestinal Microbiome - drug effects
Human Microbiome
Humans
Male
Middle Aged
Research Article
RNA, Ribosomal, 16S - genetics
Shigella
Shigella sonnei - genetics
Young Adult
16S rRNA
diarrhea
controlled human infection model
Shigella
fecal microbiome
Online AccessGet full text
ISSN2379-5042
2379-5042
DOI10.1128/msphere.00906-24

Cover

Abstract Diarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of Shigella sonnei 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent Shigella infection or recover altered microbiomes after recovery. This study is registered with ClinicalTrials.gov as NCT02816346 .
AbstractList Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all individuals exposed to Shigella or other enteropathogens have symptomatic responses, and investigating the differences between symptomatic and asymptomatic individuals can further our understanding of enteropathogen proliferation and symptomatic responses. Here, we profiled the fecal microbiomes of 45 individuals infected with Shigella sonnei strain 53G through 16S rRNA sequencing in a controlled human infection model before and during infection, after antibiotic treatment, and after clinical recovery. This model allowed for a detailed exploration of microbiome temporal dynamics during infection, as well as a comparative analysis between those with shigellosis (defined as severe symptoms caused by Shigella infection, including severe diarrhea, fever, and/or abdominal pain) and those without shigellosis. Alpha diversity decreased to a greater degree in individuals with shigellosis. Perturbations in microbial composition during infection and antibiotic treatment were significantly larger in individuals diagnosed with shigellosis than in those who were not. Participants with shigellosis had persistent changes to their microbiomes after recovery, while those without shigellosis recovered to a composition resembling their pre-infection microbiomes. These persistent changes included taxa associated with gut inflammation, such as a decrease in Faecalibacterium and an increase in Ruminococcus gnavus . Furthermore, the initial microbiomes of participants who did not develop shigellosis had a greater abundance of taxa associated with short-chain fatty acid production than participants who did develop shigellosis, including Bifidobacterium , Roseburia , and Faecalibacterium . These data could help prevent Shigella infection or symptoms.
ABSTRACT Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all individuals exposed to Shigella or other enteropathogens have symptomatic responses, and investigating the differences between symptomatic and asymptomatic individuals can further our understanding of enteropathogen proliferation and symptomatic responses. Here, we profiled the fecal microbiomes of 45 individuals infected with Shigella sonnei strain 53G through 16S rRNA sequencing in a controlled human infection model before and during infection, after antibiotic treatment, and after clinical recovery. This model allowed for a detailed exploration of microbiome temporal dynamics during infection, as well as a comparative analysis between those with shigellosis (defined as severe symptoms caused by Shigella infection, including severe diarrhea, fever, and/or abdominal pain) and those without shigellosis. Alpha diversity decreased to a greater degree in individuals with shigellosis. Perturbations in microbial composition during infection and antibiotic treatment were significantly larger in individuals diagnosed with shigellosis than in those who were not. Participants with shigellosis had persistent changes to their microbiomes after recovery, while those without shigellosis recovered to a composition resembling their pre-infection microbiomes. These persistent changes included taxa associated with gut inflammation, such as a decrease in Faecalibacterium and an increase in Ruminococcus gnavus. Furthermore, the initial microbiomes of participants who did not develop shigellosis had a greater abundance of taxa associated with short-chain fatty acid production than participants who did develop shigellosis, including Bifidobacterium, Roseburia, and Faecalibacterium. These data could help prevent Shigella infection or symptoms.IMPORTANCEDiarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of Shigella sonnei 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent Shigella infection or recover altered microbiomes after recovery.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT02816346.
Diarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of Shigella sonnei 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent Shigella infection or recover altered microbiomes after recovery. This study is registered with ClinicalTrials.gov as NCT02816346 .
Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all individuals exposed to Shigella or other enteropathogens have symptomatic responses, and investigating the differences between symptomatic and asymptomatic individuals can further our understanding of enteropathogen proliferation and symptomatic responses. Here, we profiled the fecal microbiomes of 45 individuals infected with Shigella sonnei strain 53G through 16S rRNA sequencing in a controlled human infection model before and during infection, after antibiotic treatment, and after clinical recovery. This model allowed for a detailed exploration of microbiome temporal dynamics during infection, as well as a comparative analysis between those with shigellosis (defined as severe symptoms caused by Shigella infection, including severe diarrhea, fever, and/or abdominal pain) and those without shigellosis. Alpha diversity decreased to a greater degree in individuals with shigellosis. Perturbations in microbial composition during infection and antibiotic treatment were significantly larger in individuals diagnosed with shigellosis than in those who were not. Participants with shigellosis had persistent changes to their microbiomes after recovery, while those without shigellosis recovered to a composition resembling their pre-infection microbiomes. These persistent changes included taxa associated with gut inflammation, such as a decrease in Faecalibacterium and an increase in Ruminococcus gnavus. Furthermore, the initial microbiomes of participants who did not develop shigellosis had a greater abundance of taxa associated with short-chain fatty acid production than participants who did develop shigellosis, including Bifidobacterium, Roseburia, and Faecalibacterium. These data could help prevent Shigella infection or symptoms.IMPORTANCEDiarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of Shigella sonnei 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent Shigella infection or recover altered microbiomes after recovery.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT02816346.
is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all individuals exposed to or other enteropathogens have symptomatic responses, and investigating the differences between symptomatic and asymptomatic individuals can further our understanding of enteropathogen proliferation and symptomatic responses. Here, we profiled the fecal microbiomes of 45 individuals infected with strain 53G through 16S rRNA sequencing in a controlled human infection model before and during infection, after antibiotic treatment, and after clinical recovery. This model allowed for a detailed exploration of microbiome temporal dynamics during infection, as well as a comparative analysis between those with shigellosis (defined as severe symptoms caused by infection, including severe diarrhea, fever, and/or abdominal pain) and those without shigellosis. Alpha diversity decreased to a greater degree in individuals with shigellosis. Perturbations in microbial composition during infection and antibiotic treatment were significantly larger in individuals diagnosed with shigellosis than in those who were not. Participants with shigellosis had persistent changes to their microbiomes after recovery, while those without shigellosis recovered to a composition resembling their pre-infection microbiomes. These persistent changes included taxa associated with gut inflammation, such as a decrease in and an increase in . Furthermore, the initial microbiomes of participants who did not develop shigellosis had a greater abundance of taxa associated with short-chain fatty acid production than participants who did develop shigellosis, including , , and . These data could help prevent infection or symptoms.IMPORTANCEDiarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent infection or recover altered microbiomes after recovery.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT02816346.
Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all individuals exposed to Shigella or other enteropathogens have symptomatic responses, and investigating the differences between symptomatic and asymptomatic individuals can further our understanding of enteropathogen proliferation and symptomatic responses. Here, we profiled the fecal microbiomes of 45 individuals infected with Shigella sonnei strain 53G through 16S rRNA sequencing in a controlled human infection model before and during infection, after antibiotic treatment, and after clinical recovery. This model allowed for a detailed exploration of microbiome temporal dynamics during infection, as well as a comparative analysis between those with shigellosis (defined as severe symptoms caused by Shigella infection, including severe diarrhea, fever, and/or abdominal pain) and those without shigellosis. Alpha diversity decreased to a greater degree in individuals with shigellosis. Perturbations in microbial composition during infection and antibiotic treatment were significantly larger in individuals diagnosed with shigellosis than in those who were not. Participants with shigellosis had persistent changes to their microbiomes after recovery, while those without shigellosis recovered to a composition resembling their pre-infection microbiomes. These persistent changes included taxa associated with gut inflammation, such as a decrease in Faecalibacterium and an increase in Ruminococcus gnavus. Furthermore, the initial microbiomes of participants who did not develop shigellosis had a greater abundance of taxa associated with short-chain fatty acid production than participants who did develop shigellosis, including Bifidobacterium, Roseburia, and Faecalibacterium. These data could help prevent Shigella infection or symptoms.IMPORTANCEDiarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of Shigella sonnei 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent Shigella infection or recover altered microbiomes after recovery.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT02816346.Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all individuals exposed to Shigella or other enteropathogens have symptomatic responses, and investigating the differences between symptomatic and asymptomatic individuals can further our understanding of enteropathogen proliferation and symptomatic responses. Here, we profiled the fecal microbiomes of 45 individuals infected with Shigella sonnei strain 53G through 16S rRNA sequencing in a controlled human infection model before and during infection, after antibiotic treatment, and after clinical recovery. This model allowed for a detailed exploration of microbiome temporal dynamics during infection, as well as a comparative analysis between those with shigellosis (defined as severe symptoms caused by Shigella infection, including severe diarrhea, fever, and/or abdominal pain) and those without shigellosis. Alpha diversity decreased to a greater degree in individuals with shigellosis. Perturbations in microbial composition during infection and antibiotic treatment were significantly larger in individuals diagnosed with shigellosis than in those who were not. Participants with shigellosis had persistent changes to their microbiomes after recovery, while those without shigellosis recovered to a composition resembling their pre-infection microbiomes. These persistent changes included taxa associated with gut inflammation, such as a decrease in Faecalibacterium and an increase in Ruminococcus gnavus. Furthermore, the initial microbiomes of participants who did not develop shigellosis had a greater abundance of taxa associated with short-chain fatty acid production than participants who did develop shigellosis, including Bifidobacterium, Roseburia, and Faecalibacterium. These data could help prevent Shigella infection or symptoms.IMPORTANCEDiarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of Shigella sonnei 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent Shigella infection or recover altered microbiomes after recovery.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT02816346.
Author Goodson, Michael
Porter, Chad
Baldwin, Arianna
Isidean, Sandra
Liechty, Zachary
Suvarnapunya, Akamol
Frenck, Robert
Author_xml – sequence: 1
  givenname: Zachary
  orcidid: 0000-0002-9271-6027
  surname: Liechty
  fullname: Liechty, Zachary
– sequence: 2
  givenname: Arianna
  surname: Baldwin
  fullname: Baldwin, Arianna
– sequence: 3
  givenname: Sandra
  surname: Isidean
  fullname: Isidean, Sandra
– sequence: 4
  givenname: Akamol
  surname: Suvarnapunya
  fullname: Suvarnapunya, Akamol
– sequence: 5
  givenname: Robert
  orcidid: 0000-0002-2336-526X
  surname: Frenck
  fullname: Frenck, Robert
– sequence: 6
  givenname: Chad
  surname: Porter
  fullname: Porter, Chad
– sequence: 7
  givenname: Michael
  orcidid: 0000-0002-5004-551X
  surname: Goodson
  fullname: Goodson, Michael
BackLink https://www.ncbi.nlm.nih.gov/pubmed/40152601$$D View this record in MEDLINE/PubMed
BookMark eNp1kUFv1DAQRi1UREvpnRPykUuK7dje5IRQgVKpEgfgbE3sSeJVYi92UtR_j7e7VO2B09jjp6fxfK_JSYgBCXnL2SXnovkw592ICS8Za5muhHxBzkS9aSvFpDh5cj4lFzlvGWNcC603-hU5lYwroRk_I8vn-wCzt5nGni4j0mFdaLmn2Pk4I_WB5rXbol0ytSNME4YBHf3jl5H-GP2A0wQ0xxDQU1Vf73mgNoYlxcI6Oq4zhNLti8HHQOfocHpDXvYwZbw41nPy6-uXn1ffqtvv1zdXn24rkEovlULOsGcOe4m9c4orxcQGmkborrWudtCUKrnWqgUteCskOADLHSDjrKnPyc3B6yJszS75GdK9ieDNQyOmwUBavJ3Q6B66DZeqczVIYKKz0NWiY0606BBkcX08uHZrN6OzWL4I0zPp85fgRzPEO8MFq9sSRjG8PxpS_L1iXszss90vMGBcs6l5I2Qj640uaHVAIc_CbOOaQtmT4czskzfH5M1D8kbsh3v3dLjHqf7lXAB2AEqwOSfsH5H_Ov8Cu0C_fQ
Cites_doi 10.1111/1462-2920.13023
10.1038/ajgsup.2016.9
10.3389/fimmu.2020.00906
10.1371/journal.pone.0236703
10.1371/journal.pcbi.1009442
10.1016/j.mehy.2017.07.009
10.1371/journal.pone.0074963
10.7554/eLife.45594
10.1016/j.tmaid.2013.08.008
10.1016/S1473-3099(18)30362-1
10.1093/nar/gks1219
10.1038/s41591-021-01552-x
10.1186/s13073-017-0490-5
10.1186/s12864-016-2777-0
10.1128/IAI.01021-09
10.3389/fcimb.2021.702047
10.1038/nmeth.3869
10.1016/S0140-6736(13)60844-2
10.1086/507540
10.1099/mic.0.001377
10.3389/fmicb.2016.00979
10.1093/bioinformatics/bty633
10.1080/19490976.2023.2281010
10.1016/j.cell.2016.10.043
10.4269/ajtmh.2009.80.609
10.1016/S0140-6736(16)31529-X
10.3389/fcimb.2020.589297
10.1128/mSphere.00416-20
10.1007/s00535-006-1925-8
10.1007/82_2021_242
10.7205/MILMED-D-17-00064
10.18637/jss.v082.i13
10.1093/cid/cit454
10.1093/gigascience/giz058
10.1093/bioinformatics/btm563
10.1128/mSphere.00988-19
10.1093/cid/ciz891
10.1111/j.1708-8305.2006.00009.x
10.21105/joss.01686
10.1002/9781118960608.gbm01198
10.1093/femsre/fuad039
10.1186/s40794-018-0077-1
10.3389/fpsyg.2017.00456
10.1038/s41467-022-34862-w
10.1017/S0950268812001677
10.1016/j.celrep.2023.112120
10.1016/S1473-3099(17)30276-1
10.1086/644622
10.1016/j.vaccine.2011.05.021
10.1007/82_2021_248
10.1016/j.celrep.2017.03.080
10.1038/s41435-021-00129-5
ContentType Journal Article
Copyright This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.
Copyright_xml – notice: This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.
DBID AAYXX
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
7X8
5PM
DOA
DOI 10.1128/msphere.00906-24
DatabaseName CrossRef
Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
MEDLINE - Academic
PubMed Central (Full Participant titles)
DOAJ Directory of Open Access Journals
DatabaseTitle CrossRef
MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
MEDLINE - Academic
DatabaseTitleList

CrossRef

MEDLINE
MEDLINE - Academic
Database_xml – sequence: 1
  dbid: DOA
  name: DOAJ Directory of Open Access Journals
  url: https://www.doaj.org/
  sourceTypes: Open Website
– sequence: 2
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 3
  dbid: EIF
  name: MEDLINE
  url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search
  sourceTypes: Index Database
DeliveryMethod fulltext_linktorsrc
Discipline Biology
EISSN 2379-5042
Editor Young, Vincent B.
Editor_xml – sequence: 1
  givenname: Vincent B.
  surname: Young
  fullname: Young, Vincent B.
ExternalDocumentID oai_doaj_org_article_6fab7145bd3a4a02bcab32b0d29edea4
PMC12039237
msphere00906-24
40152601
10_1128_msphere_00906_24
Genre Controlled Clinical Trial
Journal Article
Clinical Trial, Phase I
GrantInformation_xml – fundername: Military Infectious Disease Research Program
  grantid: MI230156
– fundername: Military Infectious Disease Research Program
  grantid: D0437_15_NM
– fundername: Defense Health Program Joint Program Committee-5 Working Group
– fundername: ;
– fundername: ;
  grantid: MI230156
– fundername: ;
  grantid: D0437_15_NM
GroupedDBID 0R~
53G
5VS
7X7
8FE
8FH
8FI
8FJ
AAFWJ
AAGFI
AAUOK
AAYXX
ABUWG
ADBBV
AFKRA
AFPKN
ALMA_UNASSIGNED_HOLDINGS
AOIJS
BBNVY
BCNDV
BENPR
BHPHI
BPHCQ
BVXVI
CCPQU
CITATION
DIK
EBS
FRP
FYUFA
GROUPED_DOAJ
H13
HCIFZ
HMCUK
HYE
KQ8
LK8
M48
M7P
M~E
O9-
OK1
PGMZT
PHGZM
PHGZT
PIMPY
PQGLB
PQQKQ
PROAC
R9-
RHI
RPM
RSF
UKHRP
ALIPV
CGR
CUY
CVF
ECM
EIF
NPM
7X8
PUEGO
5PM
ID FETCH-LOGICAL-a456t-5e10ef0def4efdd5155027a8826b9cd3da8b9c416659a621924adaac1dae01083
IEDL.DBID M48
ISSN 2379-5042
IngestDate Wed Aug 27 01:30:26 EDT 2025
Thu Aug 21 18:26:36 EDT 2025
Fri Sep 05 17:52:47 EDT 2025
Tue Apr 29 18:48:00 EDT 2025
Mon Jul 21 05:58:15 EDT 2025
Wed Aug 20 07:42:57 EDT 2025
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 4
Keywords 16S rRNA
diarrhea
controlled human infection model
Shigella
fecal microbiome
Language English
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-a456t-5e10ef0def4efdd5155027a8826b9cd3da8b9c416659a621924adaac1dae01083
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
The authors declare no conflict of interest.
ORCID 0000-0002-9271-6027
0000-0002-5004-551X
0000-0002-2336-526X
OpenAccessLink https://doaj.org/article/6fab7145bd3a4a02bcab32b0d29edea4
PMID 40152601
PQID 3182484376
PQPubID 23479
PageCount 14
ParticipantIDs doaj_primary_oai_doaj_org_article_6fab7145bd3a4a02bcab32b0d29edea4
pubmedcentral_primary_oai_pubmedcentral_nih_gov_12039237
proquest_miscellaneous_3182484376
asm2_journals_10_1128_msphere_00906_24
pubmed_primary_40152601
crossref_primary_10_1128_msphere_00906_24
PublicationCentury 2000
PublicationDate 2025-04-29
PublicationDateYYYYMMDD 2025-04-29
PublicationDate_xml – month: 04
  year: 2025
  text: 2025-04-29
  day: 29
PublicationDecade 2020
PublicationPlace United States
PublicationPlace_xml – name: United States
– name: 1752 N St., N.W., Washington, DC
PublicationTitle mSphere
PublicationTitleAbbrev mSphere
PublicationTitleAlternate mSphere
PublicationYear 2025
Publisher American Society for Microbiology
Publisher_xml – name: American Society for Microbiology
References e_1_3_5_27_2
e_1_3_5_25_2
e_1_3_5_23_2
e_1_3_5_21_2
e_1_3_5_44_2
e_1_3_5_46_2
e_1_3_5_29_2
Aslam A (e_1_3_5_24_2) 2024
e_1_3_5_40_2
e_1_3_5_42_2
e_1_3_5_7_2
e_1_3_5_9_2
e_1_3_5_3_2
e_1_3_5_5_2
e_1_3_5_39_2
e_1_3_5_16_2
e_1_3_5_37_2
e_1_3_5_14_2
e_1_3_5_12_2
e_1_3_5_35_2
e_1_3_5_10_2
e_1_3_5_33_2
e_1_3_5_54_2
e_1_3_5_56_2
e_1_3_5_18_2
e_1_3_5_50_2
e_1_3_5_52_2
e_1_3_5_31_2
e_1_3_5_28_2
e_1_3_5_26_2
e_1_3_5_22_2
e_1_3_5_43_2
e_1_3_5_45_2
e_1_3_5_47_2
e_1_3_5_49_2
e_1_3_5_2_2
e_1_3_5_41_2
e_1_3_5_8_2
e_1_3_5_20_2
e_1_3_5_4_2
e_1_3_5_6_2
e_1_3_5_17_2
e_1_3_5_38_2
Patterson MJ (e_1_3_5_48_2) 1996
e_1_3_5_15_2
e_1_3_5_36_2
e_1_3_5_13_2
e_1_3_5_34_2
e_1_3_5_11_2
e_1_3_5_32_2
e_1_3_5_55_2
e_1_3_5_57_2
e_1_3_5_19_2
e_1_3_5_51_2
e_1_3_5_53_2
e_1_3_5_30_2
Desai, MS, Seekatz, AM, Koropatkin, NM, Kamada, N, Hickey, CA, Wolter, M, Pudlo, NA, Kitamoto, S, Terrapon, N, Muller, A, Young, VB, Henrissat, B, Wilmes, P, Stappenbeck, TS, Núñez, G, Martens, EC (B44) 2016; 167
Stermer, E, Lubezky, A, Potasman, I, Paster, E, Lavy, A (B8) 2006; 43
Horrocks, V, King, OG, Yip, AYG, Marques, IM, McDonald, JAK (B19) 2023; 169
MacLennan, CA, Riddle, MS, Chen, WH, Talaat, KR, Jain, V, Bourgeois, AL, Frenck, R, Kotloff, K, Porter, CK (B29) 2019; 69
Stamps, BW, Kuroiwa, J, Isidean, SD, Schilling, MA, Harro, C, Talaat, KR, Sack, DA, Tribble, DR, Maue, AC, Rimmer, JE, Laird, RM, Porter, CK, Goodson, MS, Poly, F (B21) 2021; 11
Stamps, BW, Lyon, WJ, Irvin, AP, Kelley-Loughnane, N, Goodson, MS (B4) 2020; 10
Mallick, H, Rahnavard, A, McIver, LJ, Ma, S, Zhang, Y, Nguyen, LH, Tickle, TL, Weingart, G, Ren, B, Schwager, EH, Chatterjee, S, Thompson, KN, Wilkinson, JE, Subramanian, A, Lu, Y, Waldron, L, Paulson, JN, Franzosa, EA, Bravo, HC, Huttenhower, C (B38) 2021; 17
Boolchandani, M, Blake, KS, Tilley, DH, Cabada, MM, Schwartz, DJ, Patel, S, Morales, ML, Meza, R, Soto, G, Isidean, SD, Porter, CK, Simons, MP, Dantas, G (B10) 2022; 13
Hall, AB, Yassour, M, Sauk, J, Garner, A, Jiang, X, Arthur, T, Lagoudas, GK, Vatanen, T, Fornelos, N, Wilson, R, Bertha, M, Cohen, M, Garber, J, Khalili, H, Gevers, D, Ananthakrishnan, AN, Kugathasan, S, Lander, ES, Blainey, P, Vlamakis, H, Xavier, RJ, Huttenhower, C (B54) 2017; 9
Olson, S, Hall, A, Riddle, MS, Porter, CK (B6) 2019; 5
Paradis, E, Schliep, K (B36) 2019; 35
Tribble, DR, Baqar, S, Carmolli, MP, Porter, C, Pierce, KK, Sadigh, K, Guerry, P, Larsson, CJ, Rockabrand, D, Ventone, CH, Poly, F, Lyon, CE, Dakdouk, S, Fingar, A, Gilliland, T, Daunais, P, Jones, E, Rymarchyk, S, Huston, C, Darsley, M, Kirkpatrick, BD (B14) 2009; 49
Tribble, DR, Baqar, S, Scott, DA, Oplinger, ML, Trespalacios, F, Rollins, D, Walker, RI, Clements, JD, Walz, S, Gibbs, P, Burg, EF, Moran, AP, Applebee, L, Bourgeois, AL (B15) 2010; 78
Kotloff, KL, Nataro, JP, Blackwelder, WC, Nasrin, D, Farag, TH, Panchalingam, S, Wu, Y, Sow, SO, Sur, D, Breiman, RF (B24) 2013; 382
Langfelder, P, Zhang, B, Horvath, S (B39) 2008; 24
B31
Panwar, RB, Sequeira, RP, Clarke, TB (B20) 2021; 22
B35
Wickham, H, Averick, M, Bryan, J, Chang, W, McGowan, L, François, R, Grolemund, G, Hayes, A, Henry, L, Hester, J, Kuhn, M, Pedersen, T, Miller, E, Bache, S, Müller, K, Ooms, J, Robinson, D, Seidel, D, Spinu, V, Takahashi, K, Vaughan, D, Wilke, C, Woo, K, Yutani, H (B34) 2019; 4
Spiller, RC (B3) 2007; 42 Suppl 17
Parada, AE, Needham, DM, Fuhrman, JA (B30) 2016; 18
Troeger, C, Blacker, BF, Khalil, IA, Rao, PC, Cao, S, Zimsen, SR, Albertson, SB, Stanaway, JD, Deshpande, A, Abebe, Z (B1) 2018; 18
Frenck, RW, Dickey, M, Suvarnapunya, AE, Chandrasekaran, L, Kaminski, RW, Clarkson, KA, McNeal, M, Lynen, A, Parker, S, Hoeper, A, Mani, S, Fix, A, Maier, N, Venkatesan, MM, Porter, CK (B27) 2020; 5
Arnold, BF, Martin, DL, Juma, J, Mkocha, H, Ochieng, JB, Cooley, GM, Omore, R, Goodhew, EB, Morris, JF, Costantini, V, Vinjé, J, Lammie, PJ, Priest, JW (B55) 2019; 8
Porter, CK, Olson, S, Hall, A, Riddle, MS (B7) 2017; 182
Porter, CK, Riddle, MS, Tribble, DR, Louis Bougeois, A, McKenzie, R, Isidean, SD, Sebeny, P, Savarino, SJ (B18) 2011; 29
Mirzayi, C, Renson, A, Zohra, F, Elsafoury, S, Geistlinger, L, Kasselman, LJ, Eckenrode, K, van de Wijgert, J, Loughman, A, Marques, FZ (B56) 2021; 27
Aslam, A, Hashmi, MF, Okafor, CN (B23) 2024
Colombara, DV, Khalil, IA-M, Rao, PC, Troeger, C, Forouzanfar, MH, Riddle, MS, Mokdad, AH (B2) 2016; 3
Kirkpatrick, BD, Lyon, CE, Porter, CK, Maue, AC, Guerry, P, Pierce, KK, Carmolli, MP, Riddle, MS, Larsson, CJ, Hawk, D, Dill, EA, Fingar, A, Poly, F, Fimlaid, KA, Hoq, F, Tribble, DR (B16) 2013; 57
Zuo, K, Li, J, Li, K, Hu, C, Gao, Y, Chen, M, Hu, R, Liu, Y, Chi, H, Wang, H, Qin, Y, Liu, X, Li, S, Cai, J, Zhong, J, Yang, X (B53) 2019; 8
Martín, R, Rios-Covian, D, Huillet, E, Auger, S, Khazaal, S, Bermúdez-Humarán, LG, Sokol, H, Chatel, J-M, Langella, P (B51) 2023; 47
Yates, JA, Stetz, LC (B9) 2006; 13
Olgun, A (B50) 2017; 106
Porter, CK, Talaat, KR, Isidean, SD, Kardinaal, A, Chakraborty, S, Gutiérrez, RL (B17) 2021
Liu, J, Platts-Mills, JA, Juma, J, Kabir, F, Nkeze, J, Okoi, C, Operario, DJ, Uddin, J, Ahmed, S, Alonso, PL (B25) 2016; 388
Quast, C, Pruesse, E, Yilmaz, P, Gerken, J, Schweer, T, Yarza, P, Peplies, J, Glöckner, FO (B33) 2013; 41
Troeger, C, Forouzanfar, M, Rao, PC, Khalil, I, Brown, A, Reiner, RC, Fullman, N, Thompson, RL, Abajobir, A, Ahmed, M (B26) 2017; 17
Bakdash, JZ, Marusich, LR (B40) 2017; 8
Seregin, SS, Golovchenko, N, Schaf, B, Chen, J, Pudlo, NA, Mitchell, J, Baxter, NT, Zhao, L, Schloss, PD, Martens, EC, Eaton, KA, Chen, GY (B46) 2017; 19
Pop, M, Paulson, JN, Chakraborty, S, Astrovskaya, I, Lindsay, BR, Li, S, Bravo, HC, Harro, C, Parkhill, J, Walker, AW, Walker, RI, Sack, DA, Stine, OC (B22) 2016; 17
Krokowicz, L, Kaczmarek, BF, Krokowicz, P, Stojcev, Z, Mackiewicz, J, Walkowiak, J, Drews, M, Banasiewicz, T (B42) 2014; 12
Kuznetsova, A, Brockhoff, PB, Christensen, RHB (B37) 2017; 82
Patterson, MJ, Baron, S (B47) 1996
Ganesh, BP, Klopfleisch, R, Loh, G, Blaut, M (B45) 2013; 8
Rivière, A, Selak, M, Lantin, D, Leroy, F, De Vuyst, L (B41) 2016; 7
Shah, N, DuPont, HL, Ramsey, DJ (B5) 2009; 80
Walters, WA, Reyes, F, Soto, GM, Reynolds, ND, Fraser, JA, Aviles, R, Tribble, DR, Irvin, AP, Kelley-Loughnane, N, Gutierrez, RL, Riddle, MS, Ley, RE, Goodson, MS, Simons, MP (B11) 2020; 15
Kilian, KM (B48) 2015
Callahan, BJ, McMurdie, PJ, Rosen, MJ, Han, AW, Johnson, AJA, Holmes, SP (B32) 2016; 13
Sohn, J, Li, L, Zhang, L, Genco, RJ, Falkner, KL, Tettelin, H, Rowsam, AM, Smiraglia, DJ, Novak, JM, Diaz, PI, Sun, Y, Kirkwood, KL (B49) 2023; 42
Jesser, KJ, Trueba, G, Konstantinidis, KT, Levy, K (B43) 2023; 15
Parker, BJ, Wearsch, PA, Veloo, ACM, Rodriguez-Palacios, A (B52) 2020; 11
Porter, CK, Thura, N, Ranallo, RT, Riddle, MS (B12) 2013; 141
Clarkson, KA, Porter, CK, Talaat, KR, Kapulu, MC, Chen, WH, Frenck, RW (B13) 2022
Clarkson, KA, Frenck, RW, Dickey, M, Suvarnapunya, AE, Chandrasekaran, L, Weerts, HP, Heaney, CD, McNeal, M, Detizio, K, Parker, S, Hoeper, A, Bourgeois, AL, Porter, CK, Venkatesan, MM, Kaminski, RW (B28) 2020; 5
References_xml – ident: e_1_3_5_31_2
  doi: 10.1111/1462-2920.13023
– ident: e_1_3_5_3_2
  doi: 10.1038/ajgsup.2016.9
– ident: e_1_3_5_53_2
  doi: 10.3389/fimmu.2020.00906
– ident: e_1_3_5_12_2
  doi: 10.1371/journal.pone.0236703
– ident: e_1_3_5_39_2
  doi: 10.1371/journal.pcbi.1009442
– ident: e_1_3_5_51_2
  doi: 10.1016/j.mehy.2017.07.009
– ident: e_1_3_5_46_2
  doi: 10.1371/journal.pone.0074963
– ident: e_1_3_5_56_2
  doi: 10.7554/eLife.45594
– ident: e_1_3_5_43_2
  doi: 10.1016/j.tmaid.2013.08.008
– volume-title: Medical microbiology
  year: 1996
  ident: e_1_3_5_48_2
– ident: e_1_3_5_2_2
  doi: 10.1016/S1473-3099(18)30362-1
– ident: e_1_3_5_34_2
  doi: 10.1093/nar/gks1219
– ident: e_1_3_5_36_2
– ident: e_1_3_5_57_2
  doi: 10.1038/s41591-021-01552-x
– ident: e_1_3_5_55_2
  doi: 10.1186/s13073-017-0490-5
– ident: e_1_3_5_23_2
  doi: 10.1186/s12864-016-2777-0
– ident: e_1_3_5_16_2
  doi: 10.1128/IAI.01021-09
– ident: e_1_3_5_22_2
  doi: 10.3389/fcimb.2021.702047
– ident: e_1_3_5_33_2
  doi: 10.1038/nmeth.3869
– ident: e_1_3_5_32_2
– ident: e_1_3_5_25_2
  doi: 10.1016/S0140-6736(13)60844-2
– ident: e_1_3_5_9_2
  doi: 10.1086/507540
– ident: e_1_3_5_20_2
  doi: 10.1099/mic.0.001377
– ident: e_1_3_5_42_2
  doi: 10.3389/fmicb.2016.00979
– ident: e_1_3_5_37_2
  doi: 10.1093/bioinformatics/bty633
– ident: e_1_3_5_44_2
  doi: 10.1080/19490976.2023.2281010
– ident: e_1_3_5_45_2
  doi: 10.1016/j.cell.2016.10.043
– ident: e_1_3_5_6_2
  doi: 10.4269/ajtmh.2009.80.609
– ident: e_1_3_5_26_2
  doi: 10.1016/S0140-6736(16)31529-X
– ident: e_1_3_5_5_2
  doi: 10.3389/fcimb.2020.589297
– ident: e_1_3_5_28_2
  doi: 10.1128/mSphere.00416-20
– ident: e_1_3_5_4_2
  doi: 10.1007/s00535-006-1925-8
– ident: e_1_3_5_18_2
  doi: 10.1007/82_2021_242
– ident: e_1_3_5_8_2
  doi: 10.7205/MILMED-D-17-00064
– ident: e_1_3_5_38_2
  doi: 10.18637/jss.v082.i13
– ident: e_1_3_5_17_2
  doi: 10.1093/cid/cit454
– volume-title: StatPearls
  year: 2024
  ident: e_1_3_5_24_2
– ident: e_1_3_5_54_2
  doi: 10.1093/gigascience/giz058
– ident: e_1_3_5_40_2
  doi: 10.1093/bioinformatics/btm563
– ident: e_1_3_5_29_2
  doi: 10.1128/mSphere.00988-19
– ident: e_1_3_5_30_2
  doi: 10.1093/cid/ciz891
– ident: e_1_3_5_10_2
  doi: 10.1111/j.1708-8305.2006.00009.x
– ident: e_1_3_5_35_2
  doi: 10.21105/joss.01686
– ident: e_1_3_5_49_2
  doi: 10.1002/9781118960608.gbm01198
– ident: e_1_3_5_52_2
  doi: 10.1093/femsre/fuad039
– ident: e_1_3_5_7_2
  doi: 10.1186/s40794-018-0077-1
– ident: e_1_3_5_41_2
  doi: 10.3389/fpsyg.2017.00456
– ident: e_1_3_5_11_2
  doi: 10.1038/s41467-022-34862-w
– ident: e_1_3_5_13_2
  doi: 10.1017/S0950268812001677
– ident: e_1_3_5_50_2
  doi: 10.1016/j.celrep.2023.112120
– ident: e_1_3_5_27_2
  doi: 10.1016/S1473-3099(17)30276-1
– ident: e_1_3_5_15_2
  doi: 10.1086/644622
– ident: e_1_3_5_19_2
  doi: 10.1016/j.vaccine.2011.05.021
– ident: e_1_3_5_14_2
  doi: 10.1007/82_2021_248
– ident: e_1_3_5_47_2
  doi: 10.1016/j.celrep.2017.03.080
– ident: e_1_3_5_21_2
  doi: 10.1038/s41435-021-00129-5
– volume: 15
  year: 2023
  ident: B43
  article-title: Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador
  publication-title: Gut Microbes
  doi: 10.1080/19490976.2023.2281010
– volume: 27
  start-page: 1885
  year: 2021
  end-page: 1892
  ident: B56
  article-title: Reporting guidelines for human microbiome research: the STORMS checklist
  publication-title: Nat Med
  doi: 10.1038/s41591-021-01552-x
– volume: 17
  start-page: 909
  year: 2017
  end-page: 948
  ident: B26
  article-title: Estimates of global, regional, and national morbidity, mortality, and aetiologies of diarrhoeal diseases: a systematic analysis for the Global Burden of Disease Study 2015
  publication-title: Lancet Infect Dis
  doi: 10.1016/S1473-3099(17)30276-1
– volume: 12
  start-page: 183
  year: 2014
  end-page: 188
  ident: B42
  article-title: Sodium butyrate and short chain fatty acids in prevention of travellers’ diarrhoea: a randomized prospective study
  publication-title: Travel Med Infect Dis
  doi: 10.1016/j.tmaid.2013.08.008
– volume: 22
  start-page: 255
  year: 2021
  end-page: 267
  ident: B20
  article-title: Microbiota-mediated protection against antibiotic-resistant pathogens
  publication-title: Genes Immun
  doi: 10.1038/s41435-021-00129-5
– year: 2022
  ident: B13
  article-title: Shigella-controlled human infection models: current and future perspectives
  publication-title: Curr Top Microbiol Immunol
  doi: 10.1007/82_2021_248
– volume: 42
  start-page: 112120
  year: 2023
  ident: B49
  article-title: Periodontal disease is associated with increased gut colonization of pathogenic Haemophilus parainfluenzae in patients with Crohn’s disease
  publication-title: Cell Rep
  doi: 10.1016/j.celrep.2023.112120
– volume: 9
  year: 2017
  ident: B54
  article-title: A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
  publication-title: Genome Med
  doi: 10.1186/s13073-017-0490-5
– volume: 17
  year: 2016
  ident: B22
  article-title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
  publication-title: BMC Genomics
  doi: 10.1186/s12864-016-2777-0
– volume: 57
  start-page: 1106
  year: 2013
  end-page: 1113
  ident: B16
  article-title: Lack of homologous protection against Campylobacter jejuni CG8421 in a human challenge model
  publication-title: Clin Infect Dis
  doi: 10.1093/cid/cit454
– volume: 35
  start-page: 526
  year: 2019
  end-page: 528
  ident: B36
  article-title: Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bty633
– volume: 18
  start-page: 1211
  year: 2018
  end-page: 1228
  ident: B1
  article-title: Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the Global Burden of Disease Study 2016
  publication-title: Lancet Infect Dis
  doi: 10.1016/S1473-3099(18)30362-1
– volume: 82
  start-page: 1
  year: 2017
  end-page: 26
  ident: B37
  article-title: lmerTest package: tests in linear mixed effects models
  publication-title: J Stat Soft
  doi: 10.18637/jss.v082.i13
– volume: 47
  year: 2023
  ident: B51
  article-title: Faecalibacterium: a bacterial genus with promising human health applications
  publication-title: FEMS Microbiol Rev
  doi: 10.1093/femsre/fuad039
– volume: 13
  year: 2022
  ident: B10
  article-title: Impact of international travel and diarrhea on gut microbiome and resistome dynamics
  publication-title: Nat Commun
  doi: 10.1038/s41467-022-34862-w
– volume: 3
  start-page: 4
  year: 2016
  end-page: 11
  ident: B2
  article-title: Chronic health consequences of acute enteric infections in the developing world
  publication-title: Am J Gastroenterol Suppl
  doi: 10.1038/ajgsup.2016.9
– volume: 382
  start-page: 209
  year: 2013
  end-page: 222
  ident: B24
  article-title: Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study
  publication-title: The Lancet
  doi: 10.1016/S0140-6736(13)60844-2
– volume: 5
  year: 2020
  ident: B27
  article-title: Establishment of a controlled human infection model with a lyophilized strain of Shigella sonnei 53G
  publication-title: mSphere
  doi: 10.1128/mSphere.00416-20
– volume: 388
  start-page: 1291
  year: 2016
  end-page: 1301
  ident: B25
  article-title: Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study
  publication-title: Lancet
  doi: 10.1016/S0140-6736(16)31529-X
– volume: 69
  start-page: S591
  year: 2019
  end-page: S595
  ident: B29
  article-title: Consensus report on Shigella controlled human infection model: clinical endpoints
  publication-title: Clin Infect Dis
  doi: 10.1093/cid/ciz891
– year: 1996
  ident: B47
  article-title: Streptococcus
  publication-title: Medical microbiology ;4th ed ;In ;University of Texas Medical Branch at Galveston ;Galveston, TX
– ident: B31
  article-title: R Core Team . 2023 . R: a language and environment for statistical computing
– volume: 141
  start-page: 223
  year: 2013
  end-page: 232
  ident: B12
  article-title: The Shigella human challenge model
  publication-title: Epidemiol Infect
  doi: 10.1017/S0950268812001677
– start-page: 1
  year: 2015
  end-page: 47
  ident: B48
  article-title: Haemophilus
  publication-title: Bergey’s manual of systematics of archaea and bacteria ;p In ;John Wiley & Sons, Ltd
– ident: B35
  article-title: Oksanen J , Simpson G , Blanchet F , Kindt R , Legendre P , Minchin P , O’Hara RB , Solymos P , Stevens MHH , Szoecs E , et al. . 2022 . vegan: Community Ecology Package
– volume: 8
  year: 2019
  ident: B55
  article-title: Enteropathogen antibody dynamics and force of infection among children in low-resource settings
  publication-title: Elife
  doi: 10.7554/eLife.45594
– volume: 169
  year: 2023
  ident: B19
  article-title: Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization
  publication-title: Microbiology (Reading)
  doi: 10.1099/mic.0.001377
– volume: 15
  year: 2020
  ident: B11
  article-title: Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler’s diarrhea
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0236703
– volume: 80
  start-page: 609
  year: 2009
  end-page: 614
  ident: B5
  article-title: Global etiology of travelers’ diarrhea: systematic review from 1973 to the present
  publication-title: Am J Trop Med Hyg
  doi: 10.4269/ajtmh.2009.80.609
– volume: 78
  start-page: 1750
  year: 2010
  end-page: 1759
  ident: B15
  article-title: Assessment of the duration of protection in Campylobacter jejuni experimental infection in humans
  publication-title: Infect Immun
  doi: 10.1128/IAI.01021-09
– volume: 24
  start-page: 719
  year: 2008
  end-page: 720
  ident: B39
  article-title: Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btm563
– volume: 8
  year: 2013
  ident: B45
  article-title: Commensal Akkermansia muciniphila exacerbates gut inflammation in Salmonella Typhimurium-infected gnotobiotic mice
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0074963
– volume: 167
  start-page: 1339
  year: 2016
  end-page: 1353
  ident: B44
  article-title: A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility
  publication-title: Cell
  doi: 10.1016/j.cell.2016.10.043
– volume: 8
  year: 2017
  ident: B40
  article-title: Repeated measures correlation
  publication-title: Front Psychol
  doi: 10.3389/fpsyg.2017.00456
– volume: 5
  year: 2020
  ident: B28
  article-title: Immune response characterization after controlled infection with lyophilized Shigella sonnei 53G
  publication-title: mSphere
  doi: 10.1128/mSphere.00988-19
– volume: 5
  year: 2019
  ident: B6
  article-title: Travelers’ diarrhea: update on the incidence, etiology and risk in military and similar populations - 1990-2005 versus 2005-2015, does a decade make a difference?
  publication-title: Trop Dis Travel Med Vaccines
  doi: 10.1186/s40794-018-0077-1
– volume: 41
  start-page: D590
  year: 2013
  end-page: D596
  ident: B33
  article-title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gks1219
– volume: 182
  start-page: 4
  year: 2017
  end-page: 10
  ident: B7
  article-title: Travelers’ diarrhea: an update on the incidence, etiology, and risk in military deployments and similar travel populations
  publication-title: Mil Med
  doi: 10.7205/MILMED-D-17-00064
– volume: 29
  start-page: 5869
  year: 2011
  end-page: 5885
  ident: B18
  article-title: A systematic review of experimental infections with enterotoxigenic Escherichia coli (ETEC)
  publication-title: Vaccine (Auckl)
  doi: 10.1016/j.vaccine.2011.05.021
– volume: 17
  year: 2021
  ident: B38
  article-title: Multivariable association discovery in population-scale meta-omics studies
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1009442
– volume: 11
  year: 2021
  ident: B21
  article-title: Exploring changes in the host gut microbiota during a controlled human infection model for Campylobacter jejuni
  publication-title: Front Cell Infect Microbiol
  doi: 10.3389/fcimb.2021.702047
– volume: 43
  start-page: 898
  year: 2006
  end-page: 901
  ident: B8
  article-title: Is traveler’s diarrhea a significant risk factor for the development of irritable bowel syndrome? A prospective study
  publication-title: Clin Infect Dis
  doi: 10.1086/507540
– year: 2021
  ident: B17
  article-title: The controlled human infection model for enterotoxigenic Escherichia coli
  publication-title: Curr Top Microbiol Immunol
  doi: 10.1007/82_2021_242
– volume: 4
  start-page: 1686
  year: 2019
  ident: B34
  article-title: Welcome to the Tidyverse
  publication-title: JOSS
  doi: 10.21105/joss.01686
– volume: 11
  year: 2020
  ident: B52
  article-title: The genus Alistipes: gut bacteria with emerging implications to inflammation, cancer, and mental health
  publication-title: Front Immunol
  doi: 10.3389/fimmu.2020.00906
– volume: 19
  start-page: 733
  year: 2017
  end-page: 745
  ident: B46
  article-title: NLRP6 protects Il10-/- mice from colitis by limiting colonization of Akkermansia muciniphila
  publication-title: Cell Rep
  doi: 10.1016/j.celrep.2017.03.080
– volume: 13
  start-page: 581
  year: 2016
  end-page: 583
  ident: B32
  article-title: DADA2: high-resolution sample inference from Illumina amplicon data
  publication-title: Nat Methods
  doi: 10.1038/nmeth.3869
– year: 2024
  ident: B23
  article-title: Shigellosis
  publication-title: StatPearls ;In ;StatPearls Publishing ;Treasure Island, FL
– volume: 42 Suppl 17
  start-page: 41
  year: 2007
  end-page: 47
  ident: B3
  article-title: Role of infection in irritable bowel syndrome
  publication-title: J Gastroenterol
  doi: 10.1007/s00535-006-1925-8
– volume: 106
  start-page: 33
  year: 2017
  end-page: 34
  ident: B50
  article-title: “Metformin-resistant” folic acid producing probiotics or folic acid against metformin’s adverse effects like diarrhea
  publication-title: Med Hypotheses
  doi: 10.1016/j.mehy.2017.07.009
– volume: 13
  start-page: 54
  year: 2006
  end-page: 56
  ident: B9
  article-title: Reiter’s syndrome (reactive arthritis) and travelers’ diarrhea
  publication-title: J Travel Med
  doi: 10.1111/j.1708-8305.2006.00009.x
– volume: 18
  start-page: 1403
  year: 2016
  end-page: 1414
  ident: B30
  article-title: Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
  publication-title: Environ Microbiol
  doi: 10.1111/1462-2920.13023
– volume: 7
  year: 2016
  ident: B41
  article-title: Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut
  publication-title: Front Microbiol
  doi: 10.3389/fmicb.2016.00979
– volume: 10
  year: 2020
  ident: B4
  article-title: A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility
  publication-title: Front Cell Infect Microbiol
  doi: 10.3389/fcimb.2020.589297
– volume: 49
  start-page: 1512
  year: 2009
  end-page: 1519
  ident: B14
  article-title: Campylobacter jejuni strain CG8421: a refined model for the study of Campylobacteriosis and evaluation of Campylobacter vaccines in human subjects
  publication-title: Clin Infect Dis
  doi: 10.1086/644622
– volume: 8
  year: 2019
  ident: B53
  article-title: Disordered gut microbiota and alterations in metabolic patterns are associated with atrial fibrillation
  publication-title: Gigascience
  doi: 10.1093/gigascience/giz058
SSID ssj0001626676
Score 2.2936466
Snippet Diarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as...
is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all...
Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all...
Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all...
ABSTRACT Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers....
SourceID doaj
pubmedcentral
proquest
asm2
pubmed
crossref
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
StartPage e0090624
SubjectTerms 16S rRNA
Adult
Anti-Bacterial Agents - therapeutic use
Bacteria - classification
Bacteria - genetics
Bacteria - isolation & purification
controlled human infection model
diarrhea
Dysentery, Bacillary - drug therapy
Dysentery, Bacillary - microbiology
fecal microbiome
Feces - microbiology
Female
Gastrointestinal Microbiome - drug effects
Human Microbiome
Humans
Male
Middle Aged
Research Article
RNA, Ribosomal, 16S - genetics
Shigella
Shigella sonnei - genetics
Young Adult
SummonAdditionalLinks – databaseName: American Society for Microbiology Open Access
  dbid: AAUOK
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1LT9wwEB5RUKVeKloKLLSVK6FKPQQSPxLnuH1Q1Ap6KCtxs8axA5HYbEWyh_77jvPYshVCPUVKJonlz49v7PF8AEeOWLAubRHlaZFHUtksshpDkKNHIbh3qQsHnM8v0rOZ_HalrjZAjWdhhhpsjrGZdxv5q57N9cm8CUft_THxAvKDuXwCW4oYP_lcW9Pp7Mf3v4srRNPTbLUt-cCrNALTH_jabNQl7X-Iaf4bMHlvBjrdhucDdWTTHusXsOHrl_C0F5P8vQPt515cvmGLkhGtY9fLls2rPtHS3LOqZs3ShmWXhhWjhIpjYSGW_byprkMYFGtC3EvFlPga7JENkey3ZNip-bExeKtmnYbOK5idfrn8dBYNmgoRElVqI-WT2Jex86X0pXNB4IUcUySendq8cMKhpiuxtFTlmPLgnqFDLBKHnlw3LXZhs17Ufh9YSdTIZ4nVpU6k4phrIiuFzItMZE5YPoH3oYrNCKnp_A2uzYCF6bAwXE7gwwiC-dXn2HjE9mNAaWUXsmN3N6itmKGzmbREm1GZrBMoMea2QCu4jR3PvfNIH3k3YmyoN4UtEqz9YtkYGuG41JJG3Qns9ZivfkWeqAoJ2Cag11rDWlnWn9TVTZexO-Ex8VCRHfxvlRzCMx6EhmMZ8fw1bLZ3S_-G2E9r3w5t_Q_CfQVI
  priority: 102
  providerName: American Society for Microbiology
– databaseName: DOAJ Directory of Open Access Journals
  dbid: DOA
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Na9wwEBVhIZBLadK0dT-CCqHQgxtbkm3p2CRNQyC9tIHcxMiSE0PWW2rvIf--M7J32S2lvfRksAdbaEbyG2n0HmPHHlGwblydmrI2qSpclToNVOQYQEoRfOnpgPP11_LyRl3dFrcbUl9UEzbSA48dd1I24KocX-IlKMiEq8FJ4TIvTPABIhNoZrKNZCquriBOL6v1vqTQJ_OejumHj4gpMIemA-4z6Odi63cUWfv_BDV_r5jc-AVdPGVPJuzIP41t3mc7oTtgu6Oa5OMzNpyP6vI9XzQccR2_Ww583o5MS_PA2473S0frLj2vVxoqntNKLP92395RHRTvqfCl5YX8QvbAp1L2BzSMcn58Vb3V8Siic8huLj5_P7tMJ1GFFBArDWkR8iw0mQ-NCo33pPCCmSkg0C6dqb30oPGKMK0sDJSC8jPwAHXuIWDupuVzNusWXXjJeIPYKFS5041GBwkwGtFKrUxdycpLJxL2nrrYTqOitzHhENpOvrDRF1aohH1YOcH-GEk2_mJ7Sl5a2xE9dryBQWOnoLH_CpqEvVv52OJwoj0S6MJi2Vuc4oTSCqfdhL0Yfb7-FKaiBTGwJUxvRcNWW7afdO19pOzORYZAVFav_kfrX7M9QSrEmUqFecNmw89leIvQaHBHcRT8Ap5iEHQ
  priority: 102
  providerName: Directory of Open Access Journals
Title Dynamics of the gut microbiome in subjects challenged with Shigella sonnei 53G in a controlled human infection model
URI https://www.ncbi.nlm.nih.gov/pubmed/40152601
https://journals.asm.org/doi/10.1128/msphere.00906-24
https://www.proquest.com/docview/3182484376
https://pubmed.ncbi.nlm.nih.gov/PMC12039237
https://doaj.org/article/6fab7145bd3a4a02bcab32b0d29edea4
Volume 10
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3fb9MwELbYJtBe0Pg1OlhlJITEQ0ZiO4nzgFA3NiYQAwGV-madY6eLtKasSSX23-_sJIWiigeeLCV2Yvl89nf23X2EvDSIgmWh8yBL8iwQsU4DLcE5OVrgnFmTGBfg_PkiOR-Lj5N48js8uhvAeqNp5_ikxouro1_XN-9Q4d-2ATDyzax2Efj2COECmsdMbJEdf1vkHPk6sO9PXBC7J-nqrnJDw11yD82N2GXZwhUa6hlb2618Uv9NSPRvh8o_dqizPXK_g5Z01M6FB-SOrR6Suy3Z5M0j0rxvyedrOi8owj46XTZ0VraJmGaWlhWtl9ody9Q07ylWDHUHtfT7ZTl1blK0dn4xJY35B1cfaOfpfoUVPdsf7Z27Kuo5dh6T8dnpj5PzoONcCAChVBPENgptERpbCFsY4whg0HAFxOGJznLDDUgsEcUlcQYJc-YbGIA8MmDRtJP8Cdmu5pV9SmiB0MmmkZaFjETMIJMIZnKR5SlPDddsQF65IVa9zJW3R5hUnViUF4tiYkBe90JQP9scHP-oe-yktKrnsmf7B_PFVHXKqJICdIp90oaDgJDpHDRnOjQss8YCfuRFL2OF2uauUKCy82WtcAVkQgpclQdkv5X56lf91BkQuTYb1vqy_qYqL31G74iFiFN5evD_TZ-RXeaoiUMRsOw52W4WS3uIeKnRQ7KVTtIh2RmNxl8-YXl8evH129CfPgy9itwCx3ccxA
linkProvider Scholars Portal
linkToHtml http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwELagFYJLxbPd8jISQuKQNrGdxD4uj7LQBwe6Um_WOHbaoG62arIH_j0zSXbpogpxipRMEssztr8Zj-dj7K1HFKxLV0QmK0ykUpdHTgMlOQaQUgSfeTrgfHySTabq21l6doPq6yfx8l42e9DMun18GtgUiB74CPX-rKHj9mEPsQH6wkLdZZupMDGa-OZ4PP1--CfAglA9y1dbk7e8irMw_kasrUhd4f7b0ObfSZM3VqGDh2xrgI983Ov7EbsT6sfsXk8o-esJaz_1BPMNn5ccoR0_X7R8VvXFlmaBVzVvFo5CLw0vljQqnlMwlv-4qM4pFYo3lPtS8VR-IXngQzb7JQp2jH58mcBV845H5ymbHnw-_TiJBl6FCBAutVEakjiUsQ-lCqX3RPKCzikg1s6cKbz0oPGKSC1LDWSCXDTwAEXiIaD7puUztlHP67DDeInwKOSJ06VOVCrAaAQshTJFLnMvnRixd9TFdhgYje18DqHtoAvb6cIKNWLvl0qwV32djX_IfiAtreSoQnZ3Aw3GDgPOZiW4HNvkvAQFsXAFOClc7IUJPgB-5M1SxxZHFG2TQB3mi8biLCeUVjjzjth2r_PVr9AbTakI24jpNWtYa8v6k7q66Kp2JyJGLCrz3f_tktfs_uT0-MgefT05fM4eCCIejlUkzAu20V4vwktEQ617Ndj9b-Z8CZk
linkToPdf http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwELZgKxAXxJstLyMhJA5pE9tJnONCWQqFggQr9WaNY7uNxGarJnvg3zOTx9JFFeIUKXESy58f33jG8zH2yiEL1sGWUZGVRaRSm0dWAwU5epBSeJc5OuD85Tg7XKhPJ-nJJamvoQWbPWiWnSOfRva5C4Meod5fNnTc3u8hN0BbWKjrbCclZ9mE7cxmi69HfzZYkKpn-cY1ecWrOAvjX8TWitQl7r-Kbf4dNHlpFZrfYbcH-shnPd532TVf32M3ekHJX_dZe9ALzDd8FThSO366bvmy6pMtLT2vat6sLW29NLwcZVQcp81Y_v2sOqVQKN5Q7EvFU_mBygMfotl_YsFO0Y-PAVw173R0HrDF_P2Pd4fRoKsQAdKlNkp9EvsQOx-UD86RyAsap4BcO7NF6aQDjVdkallaQCbIRAMHUCYOPJpvWj5kk3pV-8eMB6RHPk-sDjpRqYBCI2EpVVHmMnfSiil7TU1sRlhNZ3MIbQYsTIeFEWrK3owgmPM-z8Y_yr4llDblKEN2dwP7ixkGnMkC2BzrZJ0EBbGwJVgpbOxE4Z0H_MjLEWODI4rcJFD71boxOMsJpRXOvFP2qMd88yu0RlNKwjZleqs3bNVl-0ldnXVZuxMRIxeV-e7_NskLdvPbwdx8_nh89ITdEqQ7HKtIFE_ZpL1Y-2dIhlr7fOj2vwHbiAk-
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Dynamics+of+the+gut+microbiome+in+subjects+challenged+with+Shigella+sonnei+53G+in+a+controlled+human+infection+model&rft.jtitle=mSphere&rft.au=Liechty%2C+Zachary&rft.au=Baldwin%2C+Arianna&rft.au=Isidean%2C+Sandra&rft.au=Suvarnapunya%2C+Akamol&rft.date=2025-04-29&rft.pub=American+Society+for+Microbiology&rft.eissn=2379-5042&rft.volume=10&rft.issue=4&rft_id=info:doi/10.1128%2Fmsphere.00906-24&rft_id=info%3Apmid%2F40152601&rft.externalDocID=PMC12039237
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2379-5042&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2379-5042&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2379-5042&client=summon