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1. The meta-gut: community coalescence of animal gut and environmental microbiomes

   https://doi.org/10.1038/s41598-021-02349-1  

   Dutton, Christopher L.; Subalusky, Amanda L.; Sanchez, Alvaro; Estrela, Sylvie; Lu, Nanxi; Hamilton, Stephen K.; Njoroge, Laban; Rosi, Emma J.; Post, David M. (November 2021, Scientific Reports)

   Abstract All animals carry specialized microbiomes, and their gut microbiota are continuously released into the environment through excretion of waste. Here we propose themeta-gutas a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and alter biogeochemical processes mediated by microbes. We demonstrate this dynamic in the hippopotamus (hippo) and the pools they inhabit. We used natural field gradients and experimental approaches to examine fecal and pool water microbial communities and aquatic biogeochemistry across a range of hippo inputs. Sequencing using 16S RNA methods revealed community coalescence between hippo gut microbiomes and the active microbial communities in hippo pools that received high inputs of hippo feces. The shared microbiome between the hippo gut and the waters into which they excrete constitutes ameta-gutsystem that could influence the biogeochemistry of recipient ecosystems and provide a reservoir of gut microbiomes that could influence other hosts. We propose thatmeta-gutdynamics may also occur where other animal species congregate in high densities, particularly in aquatic environments. 

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2. Data from: The meta-gut: community coalescence of animal gut and environmental microbiomes

   https://doi.org/10.17632/hrhy2fb7zn.1  

   Dutton, Christopher (January 2021, Mendeley)

   {"Abstract":["This is the data and R code necessary to reproduce the findings in the manuscript, "The meta-gut: community coalescence of animal gut and environmental microbiomes."\n\nHippo pool biogeochemistry and fecal and pool water microbial communities were examined through field sampling and an experiment. Sequencing using 16S RNA methods revealed that the active microbial communities in hippo pools that received high inputs of hippo feces are more similar to the hippo gut microbiome than other nearby aquatic environments. The overlap between the microbiomes of the hippo gut and the waters into which they excrete therefore constitutes a meta-gut system with potentially strong influence on the biogeochemistry of pools and downstream waters. We propose that the meta-gut may be present where other species congregate in high densities, particularly in aquatic environments, and share gut microbiota between individuals."]} 

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3. Gut mycobiome dysbiosis after sepsis and trauma

   https://doi.org/10.1186/s13054-023-04780-4  

   Park, Gwoncheol; Munley, Jennifer A; Kelly, Lauren S; Kannan, Kolenkode B; Mankowski, Robert T; Sharma, Ashish; Upchurch, Gilbert; Casadesus, Gemma; Chakrabarty, Paramita; Wallet, Shannon M; et al (December 2024, Critical Care)

   Abstract BackgroundSepsis and trauma are known to disrupt gut bacterial microbiome communities, but the impacts and perturbations in the fungal (mycobiome) community after severe infection or injury, particularly in patients experiencing chronic critical illness (CCI), remain unstudied. MethodsWe assess persistence of the gut mycobiome perturbation (dysbiosis) in patients experiencing CCI following sepsis or trauma for up to two-to-three weeks after intensive care unit hospitalization. ResultsWe show that the dysbiotic mycobiome arrays shift toward a pathobiome state, which is more susceptible to infection, in CCI patients compared to age-matched healthy subjects. The fungal community in CCI patients is largely dominated byCandidaspp; while, the commensal fungal species are depleted. Additionally, these myco-pathobiome arrays correlate with alterations in micro-ecological niche involving specific gut bacteria and gut-blood metabolites. ConclusionsThe findings reveal the persistence of mycobiome dysbiosis in both sepsis and trauma settings, even up to two weeks post-sepsis and trauma, highlighting the need to assess and address the increased risk of fungal infections in CCI patients. Graphical Abstract 

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4. Universal gut microbial relationships in the 1 gut microbiome of wild baboons

   https://doi.org/2022.08.20.504530  

   Roche, K.E.; Björk, JR.; Dasari, M.; Grieneisen, L.; Gould, T.J.; Jansen, D.; Gesquiere, L.R.; Barreiro, L.B.; Alberts, S.C.; Gilbert, J.A.; et al (January 2022, bioRxiv)

   Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships within hosts, and their generalizability across hosts, is essential to learn how microbial ecology scales up to affect microbiome assembly, dynamics, and host health. Here we gain insight into these patterns by inferring thousands of correlations in bacterial abundance between pairs of gut microbiome taxa from extensive time series data, consisting of 5,534 microbiome profiles from 56 wild baboon hosts over a 13-year period. We model these time series using a statistically robust, multinomial logistic-normal modeling framework and test the degree to which bacterial abundance correlations are consistent across hosts (i.e., "univeral") or individualized to each host. We also compare these patterns to two publicly available human data sets. We find that baboon gut microbial relationships are largely universal: correlation patterns within each baboon host reflect a mixture of idiosyncratic and shared patterns, but the shared pattern dominates by almost 2-fold. Surprisingly, the strongest and most consistently correlated bacterial pairs across hosts were overwhelmingly positively correlated and typically belonged to the same family - a 3-fold enrichment compared to pairs drawn from the data set as a whole. The bias towards universal, positive bacterial correlations was also apparent in monthly samples from human infants, and bacterial families that had universal relationships in baboons also tended to be universal in human infants. Together, our results advance our understanding of the relationships that shape gut microbial ecosystems, with implications for microbiome personalization, community assembly and stability, and the feasibility of microbiome interventions to improve host health. 

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5. The nexus of gut microbiota, diet, and health

   https://doi.org/10.31989/ffs.v2i2.885  

   Bhattarai, Sajal; Janaswamy, Srinivas (February 2022, Functional Food Science)

   The gut microbiome incorporates the ecological niche specific to the totality of the microorganisms in the human gut. Unique to every individual, the blueprint of the microbiome sets up at birth and functions as a human organ and plays a significant role in digestion, detoxification, fighting pathogens, modulating the immune system, and improving health. The gut microbiota and associated health implications are influenced by factors such as birth and age, diseases, use of antibiotics and food components (e.g., complex carbohydrates and dietary fibers, plant proteins, unsaturated fatty acids, and functional compounds of natural origin such as flavones, flavonoids, polyphenols, and antioxidants). Toward this end, diet and the gut microbiome interact and govern each other’s fate. Herein, gut dysbiosis, the alteration of natural state and composition of the gut microbiome, and the gut microflora diversity modulated by food constituents and associated health effects have been discussed. The gut microbiota composition and related metabolites are influenced by the diet which in turn modulates human health. The outcome is deemed to aid in developing personalized diet recommendations (based on the unique gut microbiome) toward improving human health. Keywords: gut microbiome, gut microbiota, gut dysbiosis, short-chain fatty acids, metabolites, health modulation 

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