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"study-abstract": "Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins, and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, Neighbor-Net networks and beta diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks, and aardwolves) even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages.",
"study-name": "Convergence of gut microbiomes in myrmecophagous mammals",
"data-origination": "SUBMITTED"
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"id": "MGYS00006747",
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"bioproject": "PRJNA693262",
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"is-private": false,
"last-update": "2025-01-27T12:47:55",
"secondary-accession": "SRP302361",
"centre-name": "Mizrahi lab, Ben-Gurion University",
"public-release-date": null,
"study-abstract": "In this study, we examine the taxonomic composition and metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using 16S amplicon sequencing and an untargeted metabolomics platform to analyze 101 fecal samples from a range of mammalian species. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species were related to the host-microbe interface, including modified and degraded host and dietary compounds. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically-distant microbiomes are more functionally diverse than redundant.",
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{
"type": "studies",
"id": "MGYS00001223",
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"accession": "MGYS00001223",
"bioproject": "PRJEB8991",
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"is-private": false,
"last-update": "2024-06-28T16:27:23",
"secondary-accession": "ERP010045",
"centre-name": "MHH",
"public-release-date": null,
"study-abstract": "The epithelium is the major entry point for many viruses but the processes protecting barrier surfaces against viral infections are incompletely understood. We identify interleukin (IL)-22 produced by group 3 innate lymphoid cells (ILC3s) as an amplifier of interferon (IFN)-lambda signaling, a synergism required to curtail replication of rotavirus, the leading cause of childhood gastroenteritis. Cooperation between IL-22 and IFN-lambda receptors, both of which are preferentially expressed by intestinal epithelial cells, was required for optimal STAT1 transcription factor activation and expression of interferon-stimulated genes. This data suggests that epithelial cells are protected against virus replication by co-opting two evolutionarily related cytokine networks. These data may inform the design of novel immunotherapies of virus infections that are sensitive to IFNs.",
"study-name": "Interferon-lambda and interleukin-22 cooperate for the induction of interferon-stimulated genes and control of rotavirus infection",
"data-origination": "SUBMITTED"
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{
"type": "studies",
"id": "MGYS00001224",
"attributes": {
"accession": "MGYS00001224",
"bioproject": "PRJEB6686",
"samples-count": 66,
"is-private": false,
"last-update": "2024-04-15T17:02:07",
"secondary-accession": "ERP006247",
"centre-name": "MHH",
"public-release-date": null,
"study-abstract": "Recent results indicate a significant contribution of innate immune signalling to maintain mucosal homeostasis but the precise underlying signal transduction pathways are ill-defined. By comparative analysis of intestinal epithelial cells isolated from conventionally raised and germ-free mice as well as animals deficient in the adaptor molecules MyD88 and TRIF, the Toll-like receptors (TLR) 3 and 4, as well as the type I and III interferon (IFN) receptors, we demonstrate significant TLR-mediated signalling under homeostatic conditions. Surprisingly, homeostatic expression of Reg3γ and Paneth cell enteric antimicrobial peptides critically relied on TRIF and in part TLR3 but was independent of IFN receptor signalling. Reduced antimicrobial peptide expression was associated with signicantly lower numbers of Paneth cells and a reduced Paneth cell maturation and differentiation factor expression in TRIF mutant compared to wildtype epithelium. This phenotype was not transferred to TRIF sufficient germ-free animals during cohousing. Low antimicrobial peptide expression in TRIF deficient mice caused reduced immediate killing of orally administered bacteria but was not associated with significant alterations in the overall composition of the enteric microbiota. The phenotype was rapidly restored in a TRIF-independent fashion after transient epithelial damage. Our results identify TRIF signalling as truly homeostatic pathway to maintain intestinal epithelial barrier function revealing fundamental differences in the innate immune signalling between mucosal homeostasis and tissue repair.",
"study-name": "TRIF signalling drives homeostatic intestinal epithelial antimicrobial peptide expression",
"data-origination": "SUBMITTED"
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"type": "studies",
"id": "MGYS00005267",
"attributes": {
"accession": "MGYS00005267",
"bioproject": "PRJEB4243",
"samples-count": 645,
"is-private": false,
"last-update": "2024-04-12T10:58:09",
"secondary-accession": "ERP003512",
"centre-name": "CCME-COLORADO",
"public-release-date": null,
"study-abstract": "International efforts to characterize the human microbiome in health and disease are producing massive amounts of data about organismal and gene content in our body habitat -associated microbial communities. A challenge is to complement these efforts with a preclinical research pipeline that tests the degree to which a person's physiologic or pathological phenotype can be ascribed to their microbiome and that offers an opportunity to evaluate potential strategies for microbiome-based therapeutics. Here we illustrate such a pre-clinical pipeline by transplanting previously frozen, uncultured fecal microbiota samples from four sets of adult female mono- and dizygotic twins discordant for obesity into groups of adult germ-free C57Bl/6J mice fed a low-fat, plant polysaccharide-rich diet. Capture of a human donor's microbiota in recipient mice is highly reproducible within and between experiments. The increased adiposity phenotype of obese co-twins is transmissible not only with the intact uncultured fecal communities, but with bacterial culture collections generated from these fecal samples. Co-housing mice five days after they received transplants of culture collections from the obese or lean member of a discordant twin pair ameliorated the increased adiposity phenotype that normally develops in recipients of the obese donor's culture collection, while having no effect on the adiposity phenotype of recipients of the lean co-twin's culture collection. These results correlate with taxonomic and metabolic changes in co-housed mice harboring the obese co-twin's culture collection. Our results demonstrate a way to perform pre-clinical studies of microbiome-associated human phenotypes, including methods for identifying, producing and testing candidate probiotic species as therapeutic or preventative agents.",
"study-name": "characterizing the gut communitties of twins discordant for obesity in gnotobiotic mice",
"data-origination": "SUBMITTED"
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"last-update": "2024-04-03T10:08:36",
"secondary-accession": "ERP138410",
"centre-name": "EMG",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA408025, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.",
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"last-update": "2024-03-29T00:04:02",
"secondary-accession": "ERP137804",
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"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA645191, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.",
"study-name": "EMG produced TPA metagenomics assembly of PRJNA645191 data set (Parity is associated with maternal gut microbiome composition during pregnancy and offspring microbiome composition in pigs).",
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"last-update": "2024-03-28T19:53:38",
"secondary-accession": "ERP138444",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA575543, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.",
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"last-update": "2024-03-28T12:30:47",
"secondary-accession": "ERP137805",
"centre-name": "EMG",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB21574, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.",
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"last-update": "2024-03-15T15:31:06",
"secondary-accession": "ERP137378",
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