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"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.",
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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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"secondary-accession": "ERP137699",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15296, 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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"secondary-accession": "ERP003513",
"centre-name": "CCME-COLORADO",
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"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",
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"secondary-accession": "ERP137368",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA677897, 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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"study-abstract": "Background: The human gut harbors around 1013-1014 microorganisms, collectively referred to as gut microbiota. Recent studies have found that the gut microbiota may have an impact on the interaction between immune regulation and anti-cancer immunotherapies.\nMethods: In order to characterize the diversity and composition of commensal microbiota and its relationship with response to immune checkpoint blockade (ICB), 16S ribosomal DNA (rDNA) sequencing was performed on 69 stool samples from advanced non-small cell lung cancer (NSCLC) patients prior to treatment with ICB.\nResults: The use of antibiotics and ICB-related skin toxicity were significantly associated with reduced gut microbiota diversity. However, antibiotics (ATB) usage was not related to low ICB efficacy. Phascolarctobacterium was enriched in patients with clinical benefit and correlated with prolonged progression-free survival, whereas Dialister was more represented in patients with progressive disease, and its higher relative abundance was associated with reduced progression-free survival and overall survival, with independent prognostic value in multivariate analysis.\nConclusions: Our results corroborate the relation between the baseline gut microbiota composition and ICB clinical outcomes in advanced NSCLC patients, and provide novel potential predictive and prognostic biomarkers for immunotherapy in NSCLC.",
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"study-abstract": "Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in gut microbial diversity, composition, and functional profiles have been described in cross-sectional studies of habitual athletes. However, this relationship is compounded by changes in diet that coincide with exercise such as dietary and supplementary protein consumption. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomic and metabolomic-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in gut microbial diversity. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement.",
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