The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

Beresford-Jones, Benjamin S.; Forster, Samuel; Stares, Mark; Notley, George; Viciani, Elisa; Browne, Hilary P.; Boehmler, Daniel J.; Soderholm, Amelia T.; Kumar, Nitin; Vervier, Kévin; Cross, Justin R.; Almeida, Alexandre; Lawley, Trevor D.; Pedicord, Virginia A.

doi:10.1016/j.chom.2021.12.003

Cited by 91 publications

(82 citation statements)

References 116 publications

(166 reference statements)

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“…Whereas a comprehensive and precise comparison at species level between the two microbiomes was not previously feasible [1,39], the comparison of CMMG with the UHGG collection reveals an overlap of only 10% of the species. In part, these findings are in agreement with the recently published Mouse Gastrointestinal Bacteria Catalogue [44], which contains 1,094 species, and shows an overlap of only 3% at the species level between human and mouse.…”

Section: Discussionsupporting

confidence: 91%

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

2022

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Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Accordingly, the similarity between human and mouse microbiomes at a low taxonomic level is not clear. We construct a comprehensive mouse microbiota genome (CMMG) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 41’798 genomes cluster into 1’573 species, of which 78.1% are uncultured, and we discovered 226 new genera, seven new families, and one new order. CMMG enables an unprecedented coverage of the mouse gut microbiome exceeding 86%, increases the mapping rate over four-fold, and allows functional microbiota analyses of human and mouse linking them to the driver species. Comparing CMMG to microbiota from the unified human gastrointestinal genomes shows an overlap of 62% at the genus but only 10% at the species level, demonstrating that human and mouse gut microbiota are largely distinct. CMMG contains the most comprehensive collection of consistently functionally annotated species of the mouse and human microbiome to date, setting the ground for the analysis of new and reanalysis of existing datasets at an unprecedented depth.

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Section: Discussionsupporting

confidence: 91%

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

2022

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“…Our collection includes multiple novel species within important bacterial groups in the mouse gut, such as the Muribaculaceae, Coriobacteriales, or Clostridiales. 2,13 Whilst this taxonomic distribution agrees overall with the diversity of isolates provided by others, 14,15 each collection brings unique diversity to light. The present work reports full-description of 39 novel taxa, including one new family represented by small-sized bacteria.…”

Section: Discussionsupporting

confidence: 83%

“…Sequences with a pairwise identity >98.7% were considered to represent the same species. MGBC 15 does not provide full-length 16S rRNA gene sequences and was not included in this analysis. (B) Shared and unique diversity within miBC, mGM, and MGBC 15 based on genomes.…”

Section: Resultsmentioning

confidence: 99%

“…The N50, longest contig, shortest contig, total number of contigs and coverage were calculated using the 'Assembly_stats.py' code available at: https://github.com/thh32/Assembly-stats. Comparison to both mGMG 14 and MGBC 15 was done using all publicly available genomes at the time of analysis (October 2021). This consisted of 108 genomes for the mGMB collection, each representing a different species, and 276 for the MMGC collection, representing 132 species.…”

Section: Genome Sequencing and Analysismentioning

confidence: 99%

“…13 Since 2016, others have gathered bacterial isolates from the mouse intestine, albeit focusing on the ob/ob mouse model commonly used to study metabolic diseases (mouse gut microbial biobank; mGMB) 14 or on functional differences between human and mouse gut microbiota (mouse gastrointestinal bacteria catalogue; MGBC). 15 Despite these studies, many bacterial species remain either undescribed or unavailable in international culture repositories. Moreover, the utility of strains from these other collections for functional studies has not been demonstrated experimentally.…”

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confidence: 99%

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Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

Afrizal

Jennings

Hitch

et al. 2022

Preprint

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Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. In this work, we expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to 212 strains, all publicly available and taxonomically described. This includes the study of strain-level diversity, small-sized bacteria, and the isolation and characterization of the first cultured members of one novel family, 10 novel genera, and 39 novel species. We demonstrate the value of this collection by performing two studies. First, metagenome-educated design of synthetic communities (SYNs) allowed establishing custom strain consortia that reflect different susceptibilities to DSS-induced colitis. Second, nine phylogenetically and functionally diverse species were used to amend the Oligo-Mouse Microbiota (OMM)12 model [Brugiroux et al. 2016 Nat Microbiol]. These strains compensated for differences observed between gnotobiotic OMM12 and specific-pathogen free (SPF) mice at multiple levels, including body composition and immune cell populations (e.g., induction of T-cell subtypes) in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks from this work are available to the community for use in future studies. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates.

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Changes in the Firmicutes to Bacteriodetes ratio in the gut microbiome in individuals with anorexia nervosa following inpatient treatment: A systematic review and a case series

Helal,

Xia,

Sardar

et al. 2024

Brain and Behavior

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ObjectiveAnorexia nervosa has the highest mortality rate among psychiatric illnesses. Current treatments remain ineffective for a large fraction of patients. This may be due to unclear mechanisms behind its development and maintenance. Studies exploring the role of the gut microbiome have revealed inconsistent evidence of dysbiosis. This article aims to investigate changes in the gut microbiome, particularly, mean differences in the Firmicutes to Bacteroidetes ratio, in adolescent and adult individuals with anorexia nervosa following inpatient treatment.MethodsLongitudinal studies investigating gut microbiome composition in inpatient populations of anorexia nervosa before and after treatment were systematically reviewed. Additionally, gut microbiome compositions were characterized in three acute anorexia nervosa inpatients early after admission and after 4–12 weeks of treatment.ResultsReview results indicated an increase in the Firmicutes to Bacteroidetes ratio in individuals with anorexia nervosa after treatment. These however did not match values of their healthy counterparts. In the case‐series samples, the reverse occurred with samples taken 4 weeks after treatment. In the patient who provided an extra sample 12 weeks after treatment, similar results to the studies included in the review were observed. Furthermore, Firmicutes to Bacteroidetes ratio values in the case‐series samples were notably higher in the two patients who had chronic anorexia nervosa.DiscussionDifferences in methodologies, small sample sizes, and insufficient data limited the generalizability of the outcomes of the reviewed studies. Results suggest a potentially unique microbiome signature in individuals with chronic anorexia nervosa, which may explain different outcomes in this group of patients.

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The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

Cited by 91 publications

References 116 publications

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

Changes in the Firmicutes to Bacteriodetes ratio in the gut microbiome in individuals with anorexia nervosa following inpatient treatment: A systematic review and a case series

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