Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China

Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.

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Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China

10.7287/peerj.preprints.27193 ◽

2018 ◽

Author(s):

Bing Zhang ◽

Jing Ren ◽

Daode Yang ◽

Shuoran Liu ◽

Xinguo Gong

Keyword(s):

Gut Microbiota ◽

Comparative Study ◽

Host Species ◽

High Throughput Sequencing ◽

Southern China ◽

Alpha Diversity ◽

Close Relationship ◽

Elaphe Carinata ◽

Deinagkistrodon Acutus

Background. The gut microbiota plays an important role in host immunity and metabolichomeostasis. Although analyses of gut microbiotas have been used to assess host health,as well as for disease prevention and treatment, no comparative study of gut microbiotasamong several species of farmed snake is yet available. In this study we characterized andcompared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosus,Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the16S rDNA gene in southern China and tested whether there was a relationship betweengut microbiotal composition and host species. Results. A total of 629 operationaltaxonomic units (OTUs) across 22 samples were detected. The dominant bacterial phylawere Bacteroidetes, Proteobacteria, Firmicutes, and Fusobacteria; the dominant bacterialgenera were Bacteroides and Cetobacterium. This was the first report of the dominance ofFusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered arelatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversityanalysis indicated that species richness and diversity were highest in the gut microbiota ofD. acutus and lowest in that of E. carinata. Significant differences in alpha diversity weredetected among the four farmed snake species. The gut microbiotas of conspecifics weremore similar to each other than to those of heterospecifics. Conclusion. This studyprovides the first comparative study of gut microbiotas among several species of farmedsnakes, and provides valuable data for the management of farmed snakes. In farmedsnakes, host species affected the species composition and diversity of the gut microbiota.

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Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China

10.7287/peerj.preprints.27193v1 ◽

2018 ◽

Author(s):

Bing Zhang ◽

Jing Ren ◽

Daode Yang ◽

Shuoran Liu ◽

Xinguo Gong

Keyword(s):

Gut Microbiota ◽

Comparative Study ◽

Host Species ◽

High Throughput Sequencing ◽

Southern China ◽

Alpha Diversity ◽

Close Relationship ◽

Elaphe Carinata ◽

Deinagkistrodon Acutus

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New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Microorganisms ◽

10.3390/microorganisms9030659 ◽

2021 ◽

Vol 9 (3) ◽

pp. 659

Author(s):

Elias Asimakis ◽

Panagiota Stathopoulou ◽

Apostolis Sapounas ◽

Kanjana Khaeso ◽

Costas Batargias ◽

...

Keyword(s):

Relative Abundance ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mutual Exclusion ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Host Diet ◽

Dominant Bacteria ◽

High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

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The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota

Microorganisms ◽

10.3390/microorganisms9020278 ◽

2021 ◽

Vol 9 (2) ◽

pp. 278

Author(s):

Shen Jean Lim ◽

Miriam Aguilar-Lopez ◽

Christine Wetzel ◽

Samia V. O. Dutra ◽

Vanessa Bray ◽

...

Keyword(s):

Gut Microbiota ◽

Preterm Infant ◽

Neonatal Intensive Care ◽

Genetic Relatedness ◽

Bovine Milk ◽

Alpha Diversity ◽

Neonatal Intensive Care Units ◽

Rrna Gene ◽

Microbial Composition ◽

Operational Taxonomic Units

The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.

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Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia

Microorganisms ◽

10.3390/microorganisms8071040 ◽

2020 ◽

Vol 8 (7) ◽

pp. 1040

Author(s):

Negash Kabtimer Bereded ◽

Manuel Curto ◽

Konrad J. Domig ◽

Getachew Beneberu Abebe ◽

Solomon Workneh Fanta ◽

...

Keyword(s):

Gut Microbiota ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Large Scale ◽

Alpha Diversity ◽

Illumina Miseq ◽

Operational Taxonomic Units ◽

Nile Tilapia Oreochromis Niloticus ◽

Miseq Platform ◽

Ethiopian Lakes

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.

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The Microbiome in Primary Sclerosing Cholangitis: Current Evidence and Potential Concepts

Seminars in Liver Disease ◽

10.1055/s-0037-1608801 ◽

2017 ◽

Vol 37 (04) ◽

pp. 314-331 ◽

Cited By ~ 27

Author(s):

Johannes Hov ◽

Tom Karlsen

Keyword(s):

Gut Microbiota ◽

Primary Sclerosing Cholangitis ◽

Sclerosing Cholangitis ◽

High Throughput Sequencing ◽

Current Evidence ◽

Published Data ◽

Sequencing Technology ◽

Close Relationship ◽

Inflammatory Bowel ◽

Host Metabolism

AbstractThe close relationship between primary sclerosing cholangitis (PSC) and inflammatory bowel disease has inspired hypothetical models in which gut bacteria or bacterial products are key players in PSC pathogenesis. Several studies using high-throughput sequencing technology to characterize the gut microbiota in PSC have been published over the past years. They all report reduced diversity and significant shifts in the overall composition of the gut microbiota. However, it remains unclear as to whether the observed changes are primary or secondary to PSC development and further studies are needed to assess the biological implications of the findings. In the present article, we review the published data in perspective of similar studies in other diseases. We discuss aspects of methodology and study design that are relevant to interpretation of the data. Furthermore, we propose that interpretation and further assessments of findings are structured into conceptual compartments, and elaborate three such possible concepts relating to immune function (the “immunobiome”), host metabolism (the “endobiome”), and dietary and xenobiotic factors (the “xenobiome”) in PSC.

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An online atlas of human plasma metabolite signatures of gut microbiome composition

10.1101/2021.12.23.21268179 ◽

2021 ◽

Author(s):

Koen F. Dekkers ◽

Sergi Sayols-Baixeras ◽

Gabriel Baldanzi ◽

Christoph Nowak ◽

Ulf Hammar ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

High Performance ◽

Alpha Diversity ◽

Plasma Metabolites ◽

Uremic Toxin ◽

Metagenomic Sequencing ◽

Microbiome Composition ◽

Plasma Metabolite

The human gut microbiota produces a variety of small compounds, some of which enter the bloodstream and impact host health. Conversely, various exogenous nutritional and pharmaceutical compounds affect the gut microbiome composition before entering circulation. Characterization of the gut microbiota—host plasma metabolite interactions is an important step towards understanding the effects of the gut microbiota on human health. However, studies involving large and deeply phenotyped cohorts that would reveal such meaningful interactions are scarce. Here, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for detailed characterization of the fecal microbiota and plasma metabolome, respectively, of 8,584 participants invited at age 50 to 64 of the Swedish CArdioPulmonary bioImage Study (SCAPIS). After adjusting for multiple comparisons, we identified 1,008 associations between species alpha diversity and plasma metabolites, and 318,944 associations between specific gut metagenomic species and plasma metabolites. The gut microbiota explained up to 50% of the variance of individual plasma metabolites (mean of 4.7%). We present all results as the searchable association atlas "GUTSY" as a rich resource for mining associations, and exemplify the potential of the atlas by presenting novel associations between oral medication and the gut microbiome, and microbiota species strongly associated with levels of the uremic toxin p-cresol sulfate. The association atlas can be used as the basis for targeted studies of perturbation of specific bacteria and for identification of candidate plasma biomarkers of gut flora composition.

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High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China

BMC Genomics ◽

10.1186/s12864-019-6219-7 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Hongling Wei ◽

Huan Wang ◽

Lei Tang ◽

Changkao Mu ◽

Chunyu Ye ◽

...

Keyword(s):

Gut Microbiota ◽

High Throughput Sequencing ◽

Southern China ◽

Scylla Paramamosain ◽

Mud Crab ◽

Sequencing Data ◽

Coastal Regions ◽

Female Crab ◽

The Core ◽

Commercially Important

Abstract Background Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health. Results Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma). Conclusions This is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.

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Host Species Determines the Composition of the Prokaryotic Microbiota in Phlebotomus Sandflies

Pathogens ◽

10.3390/pathogens9060428 ◽

2020 ◽

Vol 9 (6) ◽

pp. 428

Author(s):

Christos Papadopoulos ◽

Panagiotis A. Karas ◽

Sotirios Vasileiadis ◽

Panagiota Ligda ◽

Anastasios Saratsis ◽

...

Keyword(s):

Gut Microbiota ◽

Host Species ◽

Archaeal Community ◽

Amplicon Sequencing ◽

Structural Effect ◽

Rrna Gene ◽

Host Genotype ◽

Operational Taxonomic Units ◽

Phlebotomine Sandflies ◽

Leishmania Spp

Phlebotomine sandflies are vectors of the humans’ and mammals’ parasite Leishmania spp. Although the role of gut microbiome in the biological cycle of insects is acknowledged, we still know little about the factors modulating the composition of the gut microbiota of sandflies. We tested whether host species impose a strong structural effect on the gut microbiota of Phlebotomus spp. Sandflies were collected from the island of Leros, Greece, and classified to P. papatasi, P. neglectus, P. tobbi, and P. similis, all being negative to Leishmania spp. The prokaryotic gut microbiota was determined via 16S rRNA gene amplicon sequencing. Phlebotomus species supported distinct microbial communities (p < 0.001). P. papatasi microbiota was the most distinct over-dominated by three Spiroplasma, Wolbachia and Paenibacillus operational taxonomic units (OTUs), while another Wolbachia OTU prevailed in P. neglectus. Conversely, the microbiota of P. tobbi and P. similis was composed of several less dominant OTUs. Archaea showed low presence with the dominant OTUs belonging to methanogenic Euryarcheota, ammonia-oxidizing Thaumarcheota, and Nanoarchaeota. We provide first insights into the composition of the bacterial and archaeal community of Phlebotomus sandflies and showed that, in the absence of Leishmania, host genotype is the major modulator of Phlebotomus sandfly gut microbiota.

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Experimental infection with the hookworm, Necator americanus, promotes gut microbial diversity in human volunteers with relapsing multiple sclerosis

10.21203/rs.2.24428/v1 ◽

2020 ◽

Author(s):

Timothy Jenkins ◽

David Pritchard ◽

Radu Tanasescu ◽

Gary Telford ◽

Marina Paraiakovou ◽

...

Keyword(s):

Multiple Sclerosis ◽

Gut Microbiota ◽

Experimental Infection ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Placebo Treatment ◽

Sequencing Data ◽

Microbial Composition ◽

Necator Americanus ◽

Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been recently linked to alterations of gut microbial communities. Results In the present study we investigated, for the first time, qualitative and quantitative changes in gut microbial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus ( N+ ), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment ( PBO ). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased microbial alpha diversity in the gut microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the gut microbiota of N + individuals for which no relapses were recorded at the end of the trial. Conclusions Overall, these data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immunomodulatory properties of hookworm parasites.

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