A contribution to the larval amphibian microbiome: characterization of bacterial microbiome of Ichthyophis bannanicus (Order: Gymnophiona) and comparison with the other two amphibian orders

It is known that animal-associated microbiomes form indispensable relationships with hosts and are responsible for many functions important for host-survival. Next-gen driven approaches documenting the remarkable diversity of microbiomes have burgeoned, with amphibians too, benefiting from such treatments. The microbiome of Gymnophiona (caecilians), one of the three amphibian orders, constituting of 3% of amphibians, however, remains almost unknown. The present study aims to address this knowledge gap through analysis of the microbiome of Ichthyophis bannanicus. As these caecilian larvae are aquatic and hence exposed to a greater propensity for bacterial microbiomic interchange, we hypothesize that bacterial phyla would overlap between gut and skin. Further, from the host-specificity patterns observed in other vertebrate taxa, we hypothesize that Gymnophiona have different dominant gut bacterial microbiomes at a higher taxonomic level when compared to the larvae of the other two amphibian orders (Anura and Caudata). We used 16S rRNA gene amplicon sequencing based on Illumina Nova sequencing platform to characterize and compare the gut (represented by faecal samples) and skin microbiome of I. bannanicus larvae (N = 13), a species distributed across South-East-Asia and the only caecilian species occurring in China. We compared our gut microbiome results with published anuran and caudate larval microbiomes. For I. bannanicus, a total of 4,053 operational taxonomic units (OTU) across 13 samples were detected. Alpha-diversity indices were significant between gut and skin samples. Non-metric multidimensional scaling analysis suggest that gut and skin samples each contained a distinct microbiome at OTU level. We record significant differences between the bacterial phyla of gut and skin samples in larvae of I. bannanicus. The study provides an overview of gut and skin bacterial microbiomes of a caecilian, while highlighting the major differences between larval microbiomes of the three amphibian orders. We find a partial overlap of gut bacterial microbiomes at phylum level for the three orders; however, the relative abundance of the dominant phyla is distinct. The skin and gut microbiomes are distinct with little overlap of species, highlighting that gut-skin axis is weak. This in turn suggests that many of the microbial species on skin and gut are functionally specialized to those locations. We also show that the skin microbiome is more diverse than the gut microbiome at species level; however, a reason for this could be a portion of the gut microbiome not being represented in faecal samples. These first microbiome information from a caecilian lay the foundation for comparative studies of the three amphibian orders.

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Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

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Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

Journal of Personalized Medicine ◽

10.3390/jpm11040294 ◽

2021 ◽

Vol 11 (4) ◽

pp. 294

Author(s):

Irina Grigor’eva ◽

Tatiana Romanova ◽

Natalia Naumova ◽

Tatiana Alikina ◽

Alexey Kuznetsov ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Gallstone Disease ◽

Illumina Miseq ◽

Rrna Gene ◽

Bacterial Phyla ◽

Female Patients ◽

Composition And Structure ◽

Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

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Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Evolutionary Bioinformatics ◽

10.1177/1176934321996353 ◽

2021 ◽

Vol 17 ◽

pp. 117693432199635

Author(s):

Daoxin Liu ◽

Pengfei Song ◽

Jingyan Yan ◽

Haijing Wang ◽

Zhenyuan Cai ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

High Throughput Sequencing ◽

Tibet Plateau ◽

Rrna Gene ◽

Diversity Analysis ◽

Bacterial Phyla ◽

In Captivity ◽

Relative Abundances ◽

Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

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Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

Viruses ◽

10.3390/v13102093 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2093

Author(s):

Shen-Yuan Hsieh ◽

Mohammad A. Tariq ◽

Andrea Telatin ◽

Rebecca Ansorge ◽

Evelien M. Adriaenssens ◽

...

Keyword(s):

Alpha Diversity ◽

Diversity Indices ◽

P Value ◽

Library Preparation ◽

High Genetic Diversity ◽

Sequencing Platform ◽

Viral Genomes ◽

Healthy Donors ◽

Faecal Samples ◽

Sequencing Platforms

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

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Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet

Beneficial Microbes ◽

10.3920/bm2019.0072 ◽

2019 ◽

Vol 10 (7) ◽

pp. 811-821

Author(s):

J. Shibayama ◽

M. Goto ◽

T. Kuda ◽

M. Fukunaga ◽

H. Takahashi ◽

...

Keyword(s):

Bile Acid ◽

Rice Bran ◽

Gut Microbiome ◽

Control Diet ◽

Alpha Diversity ◽

Blood Lipid ◽

Operational Taxonomic Unit ◽

Rrna Gene ◽

High Sucrose

To clarify the effect of rice bran (RB) and fermented RB (FRB) in a high-sucrose and low-dietary fibre diet on the gut microbiome, the in vitro bile acid-lowering capacity and caecal microbiota of ICR mice fed with 20% RB or FRB diets for two weeks were determined. The caecal microbiome was analysed by 16S rRNA gene amplicon sequencing. The in vitro bile acid-lowering capacity was high for FRB. In mouse experiments, triacylglycerol and total cholesterol were generally lower with FRB, although the faecal frequency was highest in mice fed with RB. The Shannon-Wiener and Simpson’s indices for alpha-diversity in the microbiome of mice fed with RB and FRB, were higher than mice fed the control diet. At the phylum level in the caecal microbiome, Firmicutes and Bacteroidetes were high with FRB and RB, respectively. At the operational taxonomic unit level, some bacterial groups related to diabetes and gut toxicity, such as Lachnospiraceae and Enterorhabdus mucosicola, were high for RB but not for FRB diets. These results suggest that FRB, rather than RB, intake improve the intestinal environment and blood lipid condition.

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Faecal microbiota transplantation from metabolically compromised human donors accelerates osteoarthritis in mice

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2019-216471 ◽

2020 ◽

Vol 79 (5) ◽

pp. 646-656 ◽

Cited By ~ 2

Author(s):

ZeYu Huang ◽

Jing Chen ◽

BoLei Li ◽

Benhua Zeng ◽

Ching-Heng Chou ◽

...

Keyword(s):

Metabolic Syndrome ◽

Gut Microbiome ◽

Joint Damage ◽

The Other ◽

Gut Permeability ◽

Microbial Composition ◽

Germ Free ◽

Knee Oa ◽

Inflammatory Protein ◽

Faecal Samples

ObjectivesEmerging evidence suggests that the microbiome plays an important role in the pathogenesis of osteoarthritis (OA). We aimed to test the two-hit model of OA pathogenesis and potentiation in which one ‘hit’ is provided by an adverse gut microbiome that activates innate immunity; the other ‘hit’ is underlying joint damage.MethodsMedical history, faecal and blood samples were collected from human healthy controls (OA-METS-, n=4), knee OA without metabolic syndrome (OA+METS-, n=7) and knee OA with metabolic syndrome (OA+METS+, n=9). Each group of human faecal samples, whose microbial composition was identified by 16S rRNA sequencing, was pooled and transplanted into germ-free mice 2 weeks prior to meniscal/ligamentous injury (MLI) (n≥6 per group). Eight weeks after MLI, mice were evaluated for histological OA severity and synovitis, systemic inflammation and gut permeability.ResultsHistological OA severity following MLI was minimal in germ-free mice. Compared with the other groups, transplantation with the OA+METS+ microbiome was associated with higher mean systemic concentrations of inflammatory biomarkers (interleukin-1β, interleukin-6 and macrophage inflammatory protein-1α), higher gut permeability and worse OA severity. A greater abundance of Fusobacterium and Faecalibaterium and lesser abundance of Ruminococcaceae in transplanted mice were consistently correlated with OA severity and systemic biomarkers concentrations.ConclusionThe study clearly establishes a direct gut microbiome-OA connection that sets the stage for a new means of exploring OA pathogenesis and potentially new OA therapeutics. Alterations of Fusobacterium, Faecalibaterium and Ruminococcaceae suggest a role of these particular microbes in exacerbating OA.

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Alterations of gut microbiome in autoimmune hepatitis

Gut ◽

10.1136/gutjnl-2018-317836 ◽

2019 ◽

Vol 69 (3) ◽

pp. 569-577 ◽

Cited By ~ 27

Author(s):

Yiran Wei ◽

Yanmei Li ◽

Li Yan ◽

Chunyan Sun ◽

Qi Miao ◽

...

Keyword(s):

Autoimmune Hepatitis ◽

Gut Microbiome ◽

Alpha Diversity ◽

Disease Status ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Healthy Controls ◽

Microbial Composition ◽

Cross Sectional ◽

Treatment Naïve

ObjectiveThe significance of the liver-microbiome axis has been increasingly recognised as a major modulator of autoimmunity. The aim of this study was to take advantage of a large well-defined corticosteroids treatment-naïve group of patients with autoimmune hepatitis (AIH) to rigorously characterise gut dysbiosis compared with healthy controls.DesignWe performed a cross-sectional study of individuals with AIH (n=91) and matched healthy controls (n=98) by 16S rRNA gene sequencing. An independent cohort of 28 patients and 34 controls was analysed to validate the results. All the patients were collected before corticosteroids therapy.ResultsThe gut microbiome of steroid treatment-naïve AIH was characterised with lower alpha-diversity (Shannon and observed operational taxonomic units, both p<0.01) and distinct overall microbial composition compared with healthy controls (p=0.002). Depletion of obligate anaerobes and expansion of potential pathobionts including Veillonella were associated with disease status. Of note, Veillonella dispar, the most strongly disease-associated taxa (p=8.85E–8), positively correlated with serum level of aspartate aminotransferase and liver inflammation. Furthermore, the combination of four patients with AIH-associated genera distinguished AIH from controls with an area under curves of approximately 0.8 in both exploration and validation cohorts. In addition, multiple predicted functional modules were altered in the AIH gut microbiome, including lipopolysaccharide biosynthesis as well as metabolism of amino acids that can be processed by bacteria to produce immunomodulatory metabolites.ConclusionOur study establishes compositional and functional alterations of gut microbiome in AIH and suggests the potential for using gut microbiota as non-invasive biomarkers to assess disease activity.

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Impacts of Aging and Blackcurrant Supplementation on the Gut Microbiome Profile of Female Mice (P20-031-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz040.p20-031-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Sang Gil Lee ◽

Cao Lei ◽

Melissa Melough ◽

Junichi Sakaki ◽

Kendra Maas ◽

...

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

Health Benefits ◽

Alpha Diversity ◽

Young Female ◽

Rrna Gene ◽

Fecal Samples ◽

Female Mice ◽

Aged Mice ◽

Young Mice

Abstract Objectives Blackcurrant, an anthocyanin-rich berry, has multiple health benefits. The purpose of this study was to examine the impacts of blackcurrant supplementation and aging on gut bacterial communities in female mice. Methods Three-month and 18-month old female mice were provided standard chow diets with or without anthocyanin-rich blackcurrant extract (BC) (1% w/w) for four months. Upon study completion, fecal samples were collected directly from the animals’ colons. Microbiome DNA was extracted from the fecal samples and the V3-V4 regions of their 16S rRNA gene were amplified and sequenced using Results Taxonomic analysis showed a significantly decrease in alpha diversity in aged female mice, compared to young counterparts. BC consumption did not alter the alpha diversity in either young or aged mice compared to control diets. For beta diversity, we observed the clustering was associated with age but not diet. The phylogenic abundance analysis showed that the relative abundance of several phyla, including Firmicutes, Bacteroidetes, Cyanobacteria, Proteobacteria, and Tenericutes was higher in aged compared to young mice. Among them, the abundance of Firmicutes was downregulated by BC in the young but not the aged mice. The abundance of Bacteroidetes was increased by BC in both the young and the aged groups. Noticeably, Verrucomicrobia was the only phylum whose relative abundance was upregulated in the aged female mice compared to the young mice. Meanwhile, its relative abundance in the aged group was suppressed by BC. Interestingly, Desulfovibrio, which is the most representative sulfate-reducing genus, was detectable only in young female mice, and BC increased its relative abundance. Conclusions Our results characterized the gut microbiome compositions in young and aged female mice, and indicated that the gut microbiome of young and aged female mice responded differently to four month BC administration. Through additional research, the microbial alterations observed in this study should be further investigated to inform our understanding of the effect of BC on the gut microbiome, the possible health benefits related to these changes, and the differing effects of BC supplementation across populations. Funding Sources This study was supported by the USDA NIFA Seed Grant (#2016-67018-24492) and the University of Connecticut Foundation Esperance Funds to Dr. Ock K. Chun. We thank the National Institute on Aging for providing aged mice for the project and Just the Berries Ltd. for providing the blackcurrant extract.

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Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

10.1101/758359 ◽

2019 ◽

Author(s):

C Pepe-Ranney ◽

C Keyser ◽

J Trimble ◽

B Bissinger

Keyword(s):

North Carolina ◽

Community Assembly ◽

Alpha Diversity ◽

Rrna Gene ◽

Sequence Variant ◽

Skin Microbiome ◽

Microbiome Composition ◽

Pests And Diseases ◽

Sub Saharan ◽

Surrounding Soil

AbstractFarmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, ‘Beauregard’ and ‘Covington’. By comparing SSU rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil we found the skin microbiome possessed the least composition heterogeneity among samples and lowest alpha-diversity and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes.

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Changes In The Gut Microbiota After Hepatitis C Virus Eradication

10.21203/rs.3.rs-609634/v1 ◽

2021 ◽

Author(s):

Takashi Honda ◽

Masatoshi Ishigami ◽

Kenta Yamamoto ◽

Tomoaki Takeyama ◽

Takanori Ito ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Gut Microbiota ◽

Illumina Miseq ◽

Rrna Gene ◽

Virus Eradication ◽

Sequencing Platform ◽

Direct Acting Antiviral ◽

Faecal Samples ◽

Before And After

Abstract The gut microbiota interacts with infectious diseases and affects host immunity. It has also been reported that liver disease is associated with changes in the gut microbiota. To investigate changes in the gut microbiota before and after eradication of hepatitis C virus (HCV) by direct-acting antiviral (DAA) treatment in patients with chronic hepatitis C (CHC), we investigated 42 samples from 14 CHC patients who received DAA therapy for HCV. Faecal samples were obtained before treatment (Pre), when treatment ended (EOT), and 24 weeks after treatment ended (Post24). The target V3–4 region of the 16S rRNA gene from faecal samples was amplified using the Illumina Miseq sequencing platform. The diversity of the gut microbiota did not differ significantly between Pre, EOT, and Post24. PCoA analysis showed that for each patient, the values at Pre, EOT, and Post 24 were concentrated within a small area. LEfSe analysis showed that the relative abundances of Faecalibacterium and Bacillus were increased at EOT and further increased at Post24, and these genera were significantly increased at Post24 compared to Pre. These results suggest that changes in the gut microbiota need to be considered as among the various effects on living organisms observed after HCV elimination.

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