Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches
Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combinatio...
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| Published in | Genome Biology Vol. 20; no. 1; p. 96 |
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| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
BioMed Central
16.05.2019
BMC |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1474-760X 1474-7596 1474-760X |
| DOI | 10.1186/s13059-019-1711-6 |
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| Abstract | Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method. |
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| AbstractList | Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method. Abstract Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method. Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method. |
| ArticleNumber | 96 |
| Author | van Sinderen, Douwe Tatoni, Danilo Ossiprandi, Maria Cristina Alessandri, Giulia Milani, Christian Duranti, Sabrina Turroni, Francesca Lugli, Gabriele Andrea Ventura, Marco Mancabelli, Leonardo |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31097033$$D View this record in MEDLINE/PubMed |
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| Snippet | Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia.... Abstract Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial... |
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| SubjectTerms | Animal Genetics and Genomics Animals Bifidobacterium Bifidobacterium - genetics Bifidobacterium - isolation & purification Bioinformatics Biomedical and Life Sciences Callimico Callithrix Cattle computer simulation Dark matter Deoxyribonucleic acid digestive system DNA Evolutionary Biology Gastrointestinal Microbiome Genetic engineering genome Genomes Genomics Human Genetics Human gut commensals Life Sciences Metagenomics Microbial Genetics and Genomics Microbiome Biology Microbiota Microorganisms Phylogenetics Pipelines Plant Genetics and Genomics prediction Short Report species |
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| Title | Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches |
| URI | https://link.springer.com/article/10.1186/s13059-019-1711-6 https://www.ncbi.nlm.nih.gov/pubmed/31097033 https://www.proquest.com/docview/2227306988 https://www.proquest.com/docview/2232049766 https://www.proquest.com/docview/2305163710 https://pubmed.ncbi.nlm.nih.gov/PMC6524291 https://doaj.org/article/b41900f1c823400da8d0105b21c53d3a |
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