Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

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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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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Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Gut Pathogens ◽

10.1186/s13099-019-0341-6 ◽

2020 ◽

Vol 12 (1) ◽

Cited By ~ 20

Author(s):

Mohammad Tauqeer Alam ◽

Gregory C. A. Amos ◽

Andrew R. J. Murphy ◽

Simon Murch ◽

Elizabeth M. H. Wellington ◽

...

Keyword(s):

Inflammatory Bowel Disease ◽

Gut Microbiota ◽

Bowel Disease ◽

Gut Microbiome ◽

Global Scale ◽

Rrna Gene ◽

Healthy Individuals ◽

Bacterial Phyla ◽

Inflammatory Bowel ◽

Bacterial Groups

Abstract Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute > 98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of > 22,000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database (Mitchell et al. in Nucleic Acids Res 46:D726–D735, 2018). By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD.

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Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?

Pathogens ◽

10.3390/pathogens10040396 ◽

2021 ◽

Vol 10 (4) ◽

pp. 396

Author(s):

Ewa Sajnaga ◽

Marcin Skowronek ◽

Agnieszka Kalwasińska ◽

Waldemar Kazimierczak ◽

Karolina Ferenc ◽

...

Keyword(s):

Gut Microbiota ◽

Entomopathogenic Nematodes ◽

Bacterial Species ◽

Antagonistic Activity ◽

Rrna Gene ◽

Nanopore Sequencing ◽

Bacterial Phyla ◽

Melolontha Melolontha

This study focused on the potential relationships between midgut microbiota of the common cockchafer Melolontha melolontha larvae and their resistance to entomopathogenic nematodes (EPN) infection. We investigated the bacterial community associated with control and unsusceptible EPN-exposed insects through nanopore sequencing of the 16S rRNA gene. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant bacterial phyla within the complex and variable midgut microbiota of the wild M. melolontha larvae. The core microbiota was found to include 82 genera, which accounted for 3.4% of the total number of identified genera. The EPN-resistant larvae differed significantly from the control ones in the abundance of many genera belonging to the Actinomycetales, Rhizobiales, and Clostridiales orders. Additionally, the analysis of the microbiome networks revealed different sets of keystone midgut bacterial genera between these two groups of insects, indicating differences in the mutual interactions between bacteria. Finally, we detected Xenorhabdus and Photorhabdus as gut residents and various bacterial species exhibiting antagonistic activity against these entomopathogens. This study paves the way to further research aimed at unravelling the role of the host gut microbiota on the output of EPN infection, which may contribute to enhancement of the efficiency of nematodes used in eco-friendly pest management.

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Gut Microbiome Alterations in Patients With Thyroid Nodules

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.643968 ◽

2021 ◽

Vol 11 ◽

Author(s):

Ang Li ◽

Tiantian Li ◽

Xinxin Gao ◽

Hang Yan ◽

Jingfeng Chen ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Thyroid Nodules ◽

Genome Wide Association Study ◽

Adult Population ◽

Lower Grade ◽

High Grade ◽

Microbial Composition ◽

Thyroid Metabolism ◽

Relative Abundances

Thyroid nodules are found in nearly half of the adult population. Accumulating evidence suggests that the gut microbiota plays an important role in thyroid metabolism, yet the association between gut microbiota capacity, thyroid nodules, and thyroid function has not been studied comprehensively. We performed a gut microbiome genome-wide association study in 196 patients with thyroid nodules and 283 controls by using whole-genome shotgun sequencing. We found that participants with high-grade thyroid nodules have decreased number of gut microbial species and gene families compared with those with lower grade nodules and controls. There are also significant alterations in the overall microbial composition in participants with high-grade thyroid nodules. The gut microbiome in participants with high-grade thyroid nodules is characterized by greater amino acid degradation and lower butyrate production. The relative abundances of multiple butyrate producing microbes are reduced in patients with high-grade thyroid nodules and the relative abundances of L-histidine metabolism pathways are associated with thyrotropin-releasing hormone. Our study describes the gut microbiome characteristics in thyroid nodules and a gut-thyroid link and highlight specific gut microbiota as a potential therapeutic target to regulate thyroid metabolism.

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Alterations of gut microbiota in gestational diabetes patients during the second trimester of pregnancy in the Shanghai Han population

Journal of Translational Medicine ◽

10.1186/s12967-021-03040-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yao Su ◽

Hong-Kun Wang ◽

Xu-Pei Gan ◽

Li Chen ◽

Yan-Nan Cao ◽

...

Keyword(s):

Gestational Diabetes ◽

Gut Microbiota ◽

Gut Microbiome ◽

Sugar Metabolism ◽

16S Rrna Gene Sequencing ◽

Amino Sugar ◽

Fecal Microbiota ◽

Rrna Gene ◽

Second Trimester ◽

Metabolic Hormone

Abstract Background The causes of gestational diabetes mellitus (GDM) are still unclear. Recent studies have found that the imbalance of the gut microbiome could lead to disorders of human metabolism and immune system, resulting in GDM. This study aims to reveal the different gut compositions between GDM and normoglycemic pregnant women and find the relationship between gut microbiota and GDM. Methods Fecal microbiota profiles from women with GDM (n = 21) and normoglycemic women (n = 32) were assessed by 16S rRNA gene sequencing. Fasting metabolic hormone concentrations were measured using multiplex ELISA. Results Metabolic hormone levels, microbiome profiles, and inferred functional characteristics differed between women with GDM and healthy women. Additionally, four phyla and seven genera levels have different correlations with plasma glucose and insulin levels. Corynebacteriales (order), Nocardiaceae (family), Desulfovibrionaceae (family), Rhodococcus (genus), and Bacteroidetes (phylum) may be the taxonomic biomarkers of GDM. Microbial gene functions related to amino sugar and nucleotide sugar metabolism were found to be enriched in patients with GDM. Conclusion Our study indicated that dysbiosis of the gut microbiome exists in patients with GDM in the second trimester of pregnancy, and gut microbiota might be a potential diagnostic biomarker for the diagnosis, prevention, and treatment of GDM.

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Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health

10.21203/rs.3.rs-100084/v2 ◽

2021 ◽

Author(s):

Qi Yan Ang ◽

Diana L. Alba ◽

Vaibhav Upadhyay ◽

Jordan E. Bisanz ◽

Jingwei Cai ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Dietary Intake ◽

Ethnic Groups ◽

San Francisco ◽

East Asian ◽

Geographical Location ◽

Rrna Gene ◽

Bacterial Phyla ◽

Starting Point

Abstract Background: The human gut microbiota exhibits marked variation around the world, which has been attributed to dietary intake and other environmental factors. However, the degree to which ethnicity-associated differences in gut microbial community structure and function are maintained following immigration or in the context of metabolic disease is poorly understood.Results: We conducted a multi-omic study of 46 lean and obese East Asian and White participants living in the San Francisco Bay Area. 16S rRNA gene sequencing revealed significant differences between ethnic groups in bacterial richness and community structure. White individuals were enriched for the mucin-degrading Akkermansia muciniphila. East Asian participants had increased levels of multiple bacterial phyla, fermentative pathways detected by metagenomics, and the short-chain fatty acid end products acetate, propionate, and isobutyrate. Differences in the gut microbiota between the East Asian and White groups could not be explained by reported dietary intake, were more pronounced in lean individuals, and were associated with current geographical location. Microbiome transplantations into germ-free mice confirmed that the differences in the gut microbiota of the East Asian and White individuals we analyzed are independent of diet and that they differentially impact host body weight and adiposity in genetically identical mouse recipients.Conclusions: The reported findings emphasize the utility of studying diverse ethnic groups within a defined geographical location and provide a starting point for dissecting the mechanisms contributing to the complex interactions between the gut microbiome and ethnicity-associated lifestyle, demographic, metabolic, and genetic factors.

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Integrative analysis of the gut microbiome and metabolome in a rat model with stress induced irritable bowel syndrome

Scientific Reports ◽

10.1038/s41598-021-97083-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yue Hu ◽

Fang Chen ◽

Haiyong Ye ◽

Bin Lu

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Rat Model ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Metabolic Phenotype ◽

Control Group ◽

Rrna Gene ◽

Microbial Dysbiosis ◽

Irritable Bowel

AbstractStress is one of the major causes of irritable bowel syndrome (IBS), which is well-known for perturbing the microbiome and exacerbating IBS-associated symptoms. However, changes in the gut microbiome and metabolome in response to colorectal distention (CRD), combined with restraint stress (RS) administration, remains unclear. In this study, CRD and RS stress were used to construct an IBS rat model. The 16S rRNA gene sequencing was used to characterize the microbiota in ileocecal contents. UHPLC-QTOF-MS/MS assay was used to characterize the metabolome of gut microbiota. As a result, significant gut microbial dysbiosis was observed in stress-induced IBS rats, with the obvious enrichment of three and depletion of 11 bacterial taxa in IBS rats, when compared with those in the control group (q < 0.05). Meanwhile, distinct changes in the fecal metabolic phenotype of stress-induced IBS rats were also found, including five increased and 19 decreased metabolites. Furthermore, phenylalanine, tyrosine and tryptophan biosynthesis were the main metabolic pathways induced by IBS stress. Moreover, the altered gut microbiota had a strong correlation with the changes in metabolism of stress-induced IBS rats. Prevotella bacteria are correlated with the metabolism of 1-Naphthol and Arg.Thr. In conclusion, the gut microbiome, metabolome and their interaction were altered. This may be critical for the development of stress-induced IBS.

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Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

10.21203/rs.3.rs-99718/v1 ◽

2020 ◽

Author(s):

Caroline Ivanne Le Roy ◽

Alexander Kurilshikov ◽

Emily Leeming ◽

Alessia Visconti ◽

Ruth Bowyer ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Visceral Fat ◽

Gut Microbiome ◽

Body Weight Gain ◽

Healthy Eating Index ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

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Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome

Scientific Reports ◽

10.1038/s41598-019-53769-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Rafael J. Vivero ◽

Marcela Villegas-Plazas ◽

Gloria E. Cadavid-Restrepo ◽

Claudia Ximena Moreno Herrera ◽

Sandra I. Uribe ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

High Throughput Sequencing ◽

Sand Fly ◽

Human Populations ◽

Rrna Gene ◽

Remarkable Feature ◽

Core Microbiome ◽

Bacterial Phyla ◽

Wide Range

AbstractPhlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.

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The Effect of Transitioning between Feeding Methods on the Gut Microbiota Dynamics of Yaks on the Qinghai–Tibet Plateau

Animals ◽

10.3390/ani10091641 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1641

Author(s):

Xiao-Ling Zhang ◽

Tian-Wei Xu ◽

Xun-Gang Wang ◽

Yuan-Yue Geng ◽

Hong-Jin Liu ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Tibet Plateau ◽

Rrna Gene ◽

Adaptation Period ◽

Class Level ◽

Feeding Methods ◽

Rrna Gene Sequencing ◽

Gut Microbial Community ◽

Qinghai Tibet Plateau

Here we aimed to explore the change in yak gut microbiota after transferring yaks from grazing grassland to a feedlot, and determine their diet adaptation period. Five yaks were transferred from winter pasture to an indoor feedlot. Fecal samples were obtained from grazing (G) and feedlot feeding yaks at day 1 (D1), day 4 (D4), day 7 (D7), day 11 (D11), and day 16 (D16). The dynamic variation of the bacterial community was analyzed using 16S rRNA gene sequencing. The results showed that the yak gut microbial community structure underwent significant changes after diet transition. At the phylum and genus levels, most bacteria changed within D1–D11; however, no significant changes were observed from D11–D16. Furthermore, we used random forest to determine the key bacteria (at class level) disturbing gut micro-ecology. The relative abundance of the top four classes (Erysipelotrichia, Gammaproteobacteria, Saccharimonadia, and Coriobacteriia) was highest on D1–D4, and then decreased and plateaued over time. Our results demonstrated that an abrupt adjustment to a diet with high nutrition could influence the gut micro-ecology, which was stabilized within 16 days, thus providing insights into diet adaptation in the yak gut.

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