scholarly journals Host habitat is the major determinant of the gut microbiome of fish

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Pil Soo Kim ◽  
Na-Ri Shin ◽  
Jae-Bong Lee ◽  
Min-Soo Kim ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Microbial Community Composition ◽  
Terrestrial Vertebrates ◽  
Symbiotic Relationships ◽  
Machine Learning Approach ◽  
Host Habitat ◽  
Functional Profiles ◽  
Gut Microbial Community

Abstract Background Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. Results We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). Conclusions Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds.

scholarly journals Host Habitat Is the Major Determinant of the Gut Microbiome of Fish

2021 ◽  
Author(s):  
Pil Soo Kim ◽  
Na-Ri Shin ◽  
Jae-Bong Lee ◽  
Min-Soo Kim ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Microbial Community Composition ◽  
Terrestrial Vertebrates ◽  
Symbiotic Relationships ◽  
Machine Learning Approach ◽  
Host Habitat ◽  
Functional Profiles ◽  
Gut Microbial Community

Abstract Background: Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish.Results: We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).Conclusions: Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds.

Co-evolution in context: The importance of studying gut microbiomes in wild animals

2013 ◽  
Vol 1 (1) ◽  
Author(s):  
Katherine R. Amato
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Wild Animals ◽  
Natural Habitats ◽  
Host Fitness ◽  
Host Habitat ◽  
Gut Microbe ◽  
Gut Microbial Community

AbstractBecause the gut microbiota contributes to host nutrition, health and behavior, and gut microbial community composition differs according to host phylogeny, co-evolution is believed to have been an important mechanism in the formation of the host-gut microbe relationship. However, current research is not ideal for examining this theme. Most studies of the gut microbiota are performed in controlled settings, but gut microbial community composition is strongly influenced by environmental factors. To truly explore the co-evolution of host and microbe, it is necessary to have data describing host-microbe dynamics in natural environments with variation in factors such as climate, food availability, disease prevalence, and host behavior. In this review, I use current knowledge of host-gut microbe dynamics to explore the potential interactions between host and microbe in natural habitats. These interactions include the influence of host habitat on gut microbial community composition as well as the impacts of the gut microbiota on host fitness in a given habitat. Based on what we currently know, the potential connections between host habitat, the gut microbiota, and host fitness are great. Studies of wild animals will be an essential next step to test these connections and to advance our understanding of host-gut microbe co-evolution.

scholarly journals Community composition and development of the post-weaning piglet gut microbiome

2020 ◽  
Author(s):  
Daniela Gaio ◽  
Matthew Z DeMaere ◽  
Kay Anantanawat ◽  
Graeme J Eamens ◽  
Michael Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Antibiotic Treatment ◽  
Gut Microbiome ◽  
Treatment Effects ◽  
Sequence Data ◽  
Microbial Community Composition ◽  
Dominant Factor ◽  
Microbial Composition

Abstract BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. Studies have previously investigated the effects of probiotics as alternatives to antibiotic treatment for the prevention of post-weaning diarrhea. In order to describe the post-weaning gut microbiota, and the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we processed over 800 faecal time-series samples from 126 piglets and 42 sows, generating over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework.ResultsFactors such as age, litter effects, and breed, by significantly correlating with gut microbial community shifts, can be major confounding factors in the assessment of treatment effects. Intramuscular antibiotic treatment and probiotic treatments were found to correlate with alpha and beta diversity, as well as with a transient establishment of Mollicutes and Lactobacillales, respectively. We found the abundance of certain taxa to correlate with weight gain.ConclusionsOur findings demonstrate that breed, litter, and age, are important contributors to variation in the community composition, and that treatment effects of the antibiotic and probiotic treatments were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The current study shows, by means of a phylogenetic diversity framework, that the post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.

scholarly journals On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples

2021 ◽  
Author(s):  
Shan Sun ◽  
Xiangzhu Zhu ◽  
Xiang Huang ◽  
Harvey J. Murff ◽  
Reid M. Ness ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Mucosal Tissue ◽  
Tissue Samples ◽  
16S Rrna Amplicon Sequencing ◽  
Functional Profiles

AbstractThe gut microbiota plays an important role in human health and disease. Stool, swab and mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. We previously reported differences in microbial community composition with 16S rRNA amplicon sequencing between stool, swab and mucosal tissue samples. Here, we extended the previous study to a larger cohort and performed shotgun metagenome sequencing of 1,397 stool, swab and mucosal tissue samples from 240 participants. Consistent with previous results, taxonomic composition of stool and swab samples was distinct, but still more similar to each other than mucosal tissue samples, which had a substantially different community composition, characterized by a high relative abundance of the mucus metabolizers Bacteroides and Subdoligranulum, as well as bacteria with higher tolerance for oxidative stress such as Escherichia. As has been previously reported, functional profiles were more uniform across sample types than taxonomic profiles with differences between stool and swab samples smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles of different sample types were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or swab gave broadly similar results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for the experimental design of studies aimed to understand microbiota perturbations specific to defined micro niches within the human intestinal tract.

scholarly journals Host Phylogeny Determines The Gut Microbial Landscape of Cephalopods

2021 ◽  
Author(s):  
Woorim Kang ◽  
Pil Soo Kim ◽  
Euon Jung Tak ◽  
Hojun Sung ◽  
Na-Ri Shin ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Circulatory System ◽  
Illumina Miseq ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Host Phylogeny ◽  
Gut Microbial Community

Abstract BackgroundCompared to vertebrate gut microbiomes, little is known about the factors shaping the gut microbiomes in invertebrates, especially in non-insect invertebrates. Class Cephalopoda is the only group in the phylum Mollusca characterized by a closed circulatory system and a well-differentiated digestive system to process their carnivorous diet. Despite their key phylogenetic position for comparative studies as well as their ecological and commercial importances, analyses of the cephalopod gut microbiome are limited. In this study, we characterized the gut microbiota of six species of wild cephalopods by Illumina MiSeq sequencing of 16S rRNA gene amplicons.ResultsEach cephalopod gut consisted of a distinct consortium of microbes. Photobacterium and Mycoplasma were prevalent in all cephalopod hosts and were identified as core taxa. The gut microbial composition reflected host phylogeny. The importance of host phylogeny was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma, although Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Further, we showed that class Cephalopoda has a distinct gut microbial community from those of other molluscan groups. The gut microbiota of the phylum Mollusca was determined by host phylogeny, diet, and environment (aquatic vs. terrestrial).ConclusionWe provide the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of the distinctive microbes and strongly associated with their phylogeny. The genera Photobacterium and Mycoplasma are core taxa in the cephalopod gut microbiota. Collectively, our findings of this study provide evidence that cephalopod and mollusk gut microbiomes reflect phylogeny, environment, and the diet of the host and these data can be suggested to establish future directions for invertebrate gut microbiome research.

scholarly journals Adenovirus infection is associated with altered gut microbial communities in a non-human primate

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Wasimuddin ◽  
Victor M. Corman ◽  
Jörg U. Ganzhorn ◽  
Jacques Rakotondranary ◽  
Yedidya R. Ratovonamana ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Microbial Community Composition ◽  
Enteric Virus ◽  
Primate Species ◽  
Community Interactions ◽  
Microcebus Griseorufus ◽  
Gut Microbial Community ◽  
Human Primate

Abstract Adenovirus (AdV) infections are one of the main causes of diarrhea in young children. Enteric AdVs probably disrupt gut microbial defences, which can result in diarrhea. To understand the role of the gut microbiome in AdV-induced pathologies, we investigated the gut microbiome of a naturally AdV-infected non-human primate species, the Malagasy mouse lemur (Microcebus griseorufus), which represents an important model in understanding the evolution of diseases. We observed that AdV infection is associated with disruption of the gut microbial community composition. In AdV+ lemurs, several commensal taxa essential for a healthy gut microbiome decreased, whereas genera containing potential pathogens, such as Neisseria, increased in abundance. Microbial co-occurrence networks revealed a loss of important microbial community interactions in AdV+ lemurs and an overrepresentation of Prevotellaceae. The observation of enteric virus-associated loss of commensal bacteria and associated shifts towards pathobionts may represent the missing link for a better understanding of AdV-induced effects in humans, and also for their potential as drivers of co-infections, an area of research that has been largely neglected so far.

scholarly journals Host Phylogeny Determines the Gut Microbial Landscape of Cephalopods

2021 ◽  
Author(s):  
Woorim Kang ◽  
Pil Soo Kim ◽  
Euon Jung Tak ◽  
Hojun Sung ◽  
Na-Ri Shin ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Circulatory System ◽  
Illumina Miseq ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Host Phylogeny ◽  
Gut Microbial Community

Abstract Background: Compared to vertebrate gut microbiomes, little is known about the factors shaping the gut microbiomes in invertebrates, especially in non-insect invertebrates. Class Cephalopoda is the only group in the phylum Mollusca characterized by a closed circulatory system and a well-differentiated digestive system to process their carnivorous diet. Despite their key phylogenetic position for comparative studies as well as their ecological and commercial importances, analyses of the cephalopod gut microbiome are limited. In this study, we characterized the gut microbiota of six species of wild cephalopods by Illumina MiSeq sequencing of 16S rRNA gene amplicons.Results: Each cephalopod gut consisted of a distinct consortium of microbes. Photobacterium and Mycoplasma were prevalent in all cephalopod hosts and were identified as core taxa. The gut microbial composition reflected host phylogeny. The importance of host phylogeny was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma, although Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Further, we showed that class Cephalopoda has a distinct gut microbial community from those of other molluscan groups. The gut microbiota of the phylum Mollusca was determined by host phylogeny, diet, and environment (aquatic vs. terrestrial).Conclusion: We provide the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of the distinctive microbes and strongly associated with their phylogeny. The genera Photobacterium and Mycoplasma are core taxa in the cephalopod gut microbiota. Collectively, our findings of this study provide evidence that cephalopod and mollusk gut microbiomes reflect phylogeny, environment, and the diet of the host and these data can be suggested to establish future directions for invertebrate gut microbiome research.

scholarly journals Tibetan wild asses (Equus Kiang) were superior to domestic donkeys (Equus Asinus) in terms of the composition and function of gut microbial community

2019 ◽  
Author(s):  
Hongjin Liu ◽  
Xinquan Zhao ◽  
Shixiao Xu ◽  
Liang Zhao ◽  
Linyong Hu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Species Interactions ◽  
High Throughput Sequencing ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Significant Difference ◽  
And Function ◽  
Gut Microbial Community

Abstract Background: Tibetan wild asses are the only wild species of perissodactyls on the Qinghai-Tibetan Plateau, and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. The gut microbiota has a great effect on the health and nutrition of the host, however, scant research is available on the characteristics of their intestinal microbiota. Therefor, understanding the gut microbita composition and function of TWAs can provide a theoretical for the situ conservation of wild animals in the future. Results: To characterize its composition and function, we analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA regions. No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla of Bacteroidetes and Firmcutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214 , Phascolarctobacterium , Coprostanoligenes_group , Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences . Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. Conclusions: Wild asses were superior to that of domestic in gut microbial community composition and function. For wild animal conservation, wild asses are more suitable to survive in wild than to be domesticated or captive. Key words: Tibetan wild asses, domestic donkeys, 16S ribosomal RNA gene, gut microbiota

scholarly journals PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes

2021 ◽  
Vol 22 (6) ◽  
pp. 3077
Author(s):  
Zhenzhen Hao ◽  
Xiaolu Wang ◽  
Haomeng Yang ◽  
Tao Tu ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Polysaccharide ◽  
Prominent Feature ◽  
Cell Wall Polysaccharides ◽  
Gut Microbial Community

Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.

scholarly journals The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Pierre Legendre ◽  
Claude Guertin
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Strong Predictor ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Food Sources ◽  
Microbiome Composition ◽  
Living Organisms ◽  
Insect Gut ◽  
Gut Microbial Community

AbstractThe microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

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