scholarly journals Adapting to novel environments together: evolutionary and ecological correlates of the bacterial microbiome of the worlds largest cavefish diversification

2021 ◽  
Author(s):  
Shipeng Zhou ◽  
Amrapali Prithvisingh Rajput ◽  
Yewei Liu ◽  
Tingru Mao ◽  
Jian Yang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Environmental Water ◽  
Quality Parameters ◽  
Community Diversity ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Related Factors ◽  
Core Microbiome ◽  
Bacterial Microbiome ◽  
Cave Environment

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the hosts physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A to D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for six months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at clade level, with the most geographically distant clades (A and D) being the most distinct, and two geographically overlapping clades (B and C) being similar. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters was. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying adaptability and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group closely resembled that of other teleost fishes. Our results suggest that divergent selection giving rise to evolutionary novelties also includes the microbiome of these fishes, which provides a functional advantage for life in the resource-depleted cave environment.

scholarly journals Effects of functional pasta ingredients on different gut microbiota as revealed by TIM-2 in vitro model of the proximal colon

2019 ◽  
Vol 10 (3) ◽  
pp. 301-313
Author(s):  
A. Martina ◽  
G.E. Felis ◽  
M. Corradi ◽  
C. Maffeis ◽  
S. Torriani ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
In Vitro Model ◽  
Bacillus Coagulans ◽  
Proximal Colon ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Dietary Interventions ◽  
Vitro Model ◽  
Microbial Groups

Diet-related modulation of gut microbiota and its metabolic activity represents an intriguing research context, particularly in the case of disorders related to imbalances in gut microbial communities. We here explored the effects of Bacillus coagulans GBI-30, 6086 (BC30), β-glucans, and innovative whole-grain pastas, with or without these functional ingredients, on gut microbiota from three groups of children, presenting different susceptibility to type 1 diabetes, by using the well-controlled TNO in vitro model of the proximal colon (TIM-2). Short- and branched-chain fatty acids production and microbiota composition were assessed by means of gas chromatography and 16S rRNA gene profiling, respectively. In most cases, in vitro dietary interventions caused microbiota-dependent modulations as a result of intergroup variability, but also specific changes in microbial groups were shared between the three microbiotas, highlighting specific diet-microbial taxa connections.

scholarly journals Gut microbiota features of the geographically diverse Indian population

2018 ◽  
Author(s):  
Sudarshan A. Shetty
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Indian Population ◽  
Geographic Location ◽  
Population Level ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Base Line ◽  
Microbiome Composition ◽  
And Function

AbstractPopulation-level microbial profiling allows for identifying the overarching features of the microbiome. Knowledge of population specific base-line gut microbiome features is important due to the widely reported impact of geography, lifestyle and dietary patterns on the microbiome composition, structure and function. Here, the gut microbiota of more than 1000 subjects across the length and breadth of India is presented. The publicly available 16S rRNA gene profiling data of faecal microbiota from the Landscape Of Gut Microbiome - Pan-India Exploration (LogMPIE) study representing 14 major cities, covering populations from northern, southern, eastern and western part of India analyzed. Majority of the dominant OTUs belonged to the Firmicutes, Bacteroidetes and Proteobacteria phyla. The rarer fraction was comprised of OTUs mainly from the phyla Verrucomicrobia and Spirochaetes. The median core size was estimated to consist of 12 OTUs (>80% prevalence) dominated by representing genera Prevotella, Faecalibacterium, Bacteroides, Roseburia, Megasphaera, Eubacterium and Gemmiger. Geographic location explained majority of the variation in the gut microbiota community structure. The observations of the present study support the previous reports of Prevotella dominance in the Indian population. The Prevotella/Bacteroides ratio was high for the overall population irrespective of geographic location and did not correlate with BMI or age of the participants. Despite a rapid transition towards a western lifestyle, high prevalence of Treponema in the Indian gut microbiota suggests that the urban population still harbors signatures of the traditional gut microbiome. The results presented here improve the knowledge of baseline microbiota in the Indian population across the length and breadth of the country. This study provides a base for future studies which need to incorporate numerous other confounding factors and their impact on the observed characteristics of the Indian gut microbiome.

scholarly journals Rubidium chloride modulated the intestinal microbiota community in mice

2020 ◽  
Author(s):  
Qian Chen ◽  
Zhiguo He ◽  
Yuting Zhuo ◽  
Shuzhen Li ◽  
Wenjing Yang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Sulfate Reducing Bacteria ◽  
Community Diversity ◽  
Microbial Composition ◽  
Intestinal Microbes ◽  
Sulfate Reducing ◽  
Bacterial Microbiome ◽  
Reducing Bacteria ◽  
First Time

Abstract Background The intestinal microbiota plays an important role in host health. Although rubidium (Rb) has been used to study for depression and cancers, the interaction between intestinal microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and intestinal microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated of their characteristics and bacterial microbiome changes. Results The 16S ribosomal RNA gene sequencing of feces showed RbCl generally maintained the microbial community diversity, while the shifts in gut microbial composition were apparent after RbCl exposure for the first time. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio. While, RbCl significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. Besides, with regarding to the composition of archaea, RbCl significantly enhanced the abundances of Crenarchaeota, Thermoprotei, Sulfolobales, Sulfolobaceae and Sulfolobus lineages. Conclusions These results revealed that enrichments of Clostridium XlVa, Alistipes and sulfate-reducing bacteria could act on brain-gut-microbiota axis by affecting serotonergic system and immune system. Therefore, it was likely that RbCl would have beneficial anti-effects on depression and cancers by modifying brain-gut-microbiota axis.

scholarly journals Urinary TMAO Levels Are Associated with the Taxonomic Composition of the Gut Microbiota and with the Choline TMA-Lyase Gene (cutC) Harbored by Enterobacteriaceae

Nutrients ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 62 ◽  
Author(s):  
Alessandro Dalla Via ◽  
Giorgio Gargari ◽  
Valentina Taverniti ◽  
Greta Rondini ◽  
Ilaria Velardi ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Method Development ◽  
Ultra Performance Liquid Chromatography ◽  
Taxonomic Composition ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Two Factors ◽  
Polymerase Chain ◽  
Dietary Choline

Gut microbiota metabolization of dietary choline may promote atherosclerosis through trimethylamine (TMA), which is rapidly absorbed and converted in the liver to proatherogenic trimethylamine-N-oxide (TMAO). The aim of this study was to verify whether TMAO urinary levels may be associated with the fecal relative abundance of specific bacterial taxa and the bacterial choline TMA-lyase gene cutC. The analysis of sequences available in GenBank grouped the cutC gene into two main clusters, cut-Dd and cut-Kp. A quantitative real-time polymerase chain reaction (qPCR) protocol was developed to quantify cutC and was used with DNA isolated from three fecal samples collected weekly over the course of three consecutive weeks from 16 healthy adults. The same DNA was used for 16S rRNA gene profiling. Concomitantly, urine was used to quantify TMAO by ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). All samples were positive for cutC and TMAO. Correlation analysis showed that the cut-Kp gene cluster was significantly associated with Enterobacteriaceae. Linear mixed models revealed that urinary TMAO levels may be predicted by fecal cut-Kp and by 23 operational taxonomic units (OTUs). Most of the OTUs significantly associated with TMAO were also significantly associated with cut-Kp, confirming the possible relationship between these two factors. In conclusion, this preliminary method-development study suggests the existence of a relationship between TMAO excreted in urine, specific fecal bacterial OTUs, and a cutC subgroup ascribable to the choline-TMA conversion enzymes of Enterobacteriaceae.

scholarly journals Neurodevelopment correlates with gut microbiota in a cross-sectional analysis of children at 3 years of age in rural China

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sarah E. Rothenberg ◽  
Qiurong Chen ◽  
Jian Shen ◽  
Yanfen Nong ◽  
Hua Nong ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Infant Development ◽  
Rural China ◽  
Alpha Diversity ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Linear Regression Models ◽  
Cross Sectional ◽  
Developmental Index ◽  
Bayley Scales

AbstractWe investigated cross-sectional associations between children’s neurodevelopment and their gut microbiota composition. Study children (36 months of age) lived in rural China (n = 46). Neurodevelopment was assessed using the Bayley Scales of Infant Development, 2nd Edition, yielding the Mental Developmental Index (MDI) and Psychomotor Developmental Index (PDI). Children's gut microbiota was assessed using 16S rRNA gene profiling. Microbial diversity was characterized using alpha diversity patterns. Additionally, 3 coabundance factors were determined for the 25 most abundant taxa. Multivariable linear regression models were constructed to examine the relationships between Bayley scores (MDI and PDI) and children's gut microbiota. In adjusted models, MDI and PDI scores were not associated with alpha diversity indices. However, in adjusted models, MDI and PDI scores were positively associated with the first coabundance factor, which captured positive loadings for the genera Faecalibacterium, Sutterella, and Clostridium cluster XIVa. For an interquartile range increase in the first coabundance factor, MDI scores increased by 3.9 points [95% confidence interval (CI): 0, 7.7], while PDI scores increased by 8.6 points (95% CI 3.1, 14). Our results highlight the potential for gut microbial compositional characteristics to be important correlates of children's Bayley Scales performance at 36 months of age.

scholarly journals Effect of dietary folate level on organ weight, digesta pH, short-chain fatty acid concentration, and intestinal microbiota of weaned piglets

2021 ◽  
Vol 99 (1) ◽  
Author(s):  
Lei Wang ◽  
Lijun Zou ◽  
Jianzhong Li ◽  
Huansheng Yang ◽  
Yulong Yin
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Organ Weight ◽  
Community Diversity ◽  
Short Chain ◽  
Control Group ◽  
Rrna Gene ◽  
Weaned Piglets ◽  
Folate Supplementation ◽  
Stomach Ph

Abstract Folate is increasingly thought to promote gastrointestinal health and regulate the diversity of gut microbiota to alleviate weaning stress in piglets. The present study was conducted to investigate the effects of folate on organ weight, digesta pH, short-chain fatty acids (SCFAs) concentration, and intestinal microbiota in weaned piglets. A total of 28 piglets (6.73 ± 0.62 kg) were allocated to four dietary treatments consisting of a control group, 3, 9, and 18 mg/kg of folate supplementation in a 14-d feeding trial. The results showed that piglets fed with 9 and 18 mg/kg of folate supplementation had greater (P < 0.05) average liver and spleen weight than the control group. Folate supplementation (9 and 18 mg/kg) can significantly increase (P < 0.05) the stomach pH and tend (P < 0.10) to decrease the cecum pH. Folate treatment (9 and 18 mg/kg) had a positive effect on the metabolism of SCFAs in piglets, in particular, compared with the control group, and the content of acetic acid (AA) and valeric acid was markedly increased (P < 0.05) in the cecum and colon, respectively. Moreover, isobutyric acid, butyric acid, and isovaleric acid were tended (P < 0.10) to increase in the colon. Cecum contents samples were used to determine bacterial community diversity by 16S rRNA gene amplicon sequencing. At the genus level, in the cecum, there was a higher (P < 0.05) relative abundance of Lactobacillus reuteri, Lactobacillus salivarius, and Lactobacillus mucosae in the 9 mg/kg folate supplementation group. The functional pathways analysis predicted that folate may modify nutrient metabolism by changing the gut microbiota function of weaned piglets. Furthermore, the data showed that Lactobacillus was positively correlated with AA in the cecum. Overall, these findings suggested that folate treatment could increase the organ weight and the stomach pH of weaned piglets and had beneficial effects on gut health, which might be attributed to the alteration in intestinal microbiota induced by folate and the interaction of the intestinal microbiota with SCFAs.

scholarly journals Rubidium chloride modulated the fecal microbiota community in mice

2020 ◽  
Author(s):  
Qian Chen ◽  
Zhiguo He ◽  
Yuting Zhuo ◽  
Shuzhen Li ◽  
Wenjing Yang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Fecal Microbiota ◽  
Community Diversity ◽  
Microbial Composition ◽  
Sulfate Reducing ◽  
Host Health ◽  
Bacterial Microbiome ◽  
Reducing Bacteria ◽  
First Time ◽  
The Relationship

Abstract Background: The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study for depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated of their characteristics and bacterial microbiome changes.Results: The 16S ribosomal RNA gene sequencing of feces showed RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure for the first time. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio. While, RbCl significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. Besides, with regarding to the composition of archaea, RbCl significantly enhanced the abundances of Crenarchaeota, Thermoprotei, Sulfolobales, Sulfolobaceae and Sulfolobus lineages. Conclusions: These results revealed that enrichments of Clostridium XlVa and Alistipes could affect the levels of serotonin, a critical signaling molecule of brain-gut-microbiota axis. Therefore, anticancer and anti-depressant effects of RbCl might be partly mediated by modifying brain-gut-microbiota axis.

scholarly journals Seasonal Variation in Gut Microbiota Composition: Comparative Analysis of Siberian Musk Deer (Moschus moschiferus) and Forest Musk Deer (Moschus berezovskii)

2020 ◽  
Author(s):  
Rina Su ◽  
Myagmarsuren Erdenedalai ◽  
Menggen Dalai ◽  
L Batkhuu ◽  
Chimedragchaa Chi ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Rapid Development ◽  
Community Diversity ◽  
Food Sources ◽  
Rrna Gene ◽  
Musk Deer ◽  
Deer Population ◽  
Seasonal Factors ◽  
Α Diversity ◽  
Significant Difference

Abstract Background: Musk deer is famous for its secretion of musk, but due to various factors that the musk deer population has dropped sharply and it is difficult to expand herd sizes. In light of the rapid development of agriculture and technology, as well as the urgent need for wildlife conservation, research on the gut microbiota of musk deer is warranted. The gut microbiota impacts host health is shaped by dietary, environmental, and host factors.Results: We studied the gut microbiota in Siberian musk and Forest musk deer using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene. Fecal samples were collected during two seasons to determine associations between community diversity, composition, and seasonal factors. The results show that the Firmicutes and Bacteroidetes were the predominant phyla in both species, their relative abundance was significantly different with species and seasonal factors. The Siberian musk deer population sampled in this study had a wider feeding range and no dietary limitations. Affected by the richness and type of food sources, the microbial α-diversity is higher in summer than winter. In the siberian musk deer have only Tenericutes significant difference with the season change. Conclusions:The gut bacterial composition of these two musk deer is significantly different, and the abundance of core bacteria is affected by seasonal factors. This study is the first to analyze the composition of the gut microflora in Siberian musk deer, and these results provide a foundation for improving feeding for musk deer populations and further studies investigating the environmental impact of musk deer.

scholarly journals Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

2021 ◽  
Vol 11 ◽  
Author(s):  
Gaël Even ◽  
Ana Lokmer ◽  
Jules Rodrigues ◽  
Christophe Audebert ◽  
Eric Viscogliosi ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Experimental Studies ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Sequencing Data ◽  
Human Gut ◽  
Bacterial Microbiota ◽  
Bacterial Microbiome ◽  
Blastocystis Sp

Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis, the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural “traditional” populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae, Coprococcus and Butyrivibrio) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba-negative and Entamoeba-positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis, our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions.

scholarly journals Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission

Nutrients ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 278 ◽  
Author(s):  
Karina Al Assal ◽  
Edi Prifti ◽  
Eugeni Belda ◽  
Priscila Sala ◽  
Karine Clément ◽  
...  
Keyword(s):  
Gastric Bypass ◽  
Food Intake ◽  
Gut Microbiota ◽  
Characteristic Curve ◽  
Diabetes Remission ◽  
Gut Bacteria ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Before And After ◽  
Type 2 Diabetes Remission

Gut microbiota composition is influenced by environmental factors and has been shown to impact body metabolism. Objective: To assess the gut microbiota profile before and after Roux-en-Y gastric bypass (RYGB) and the correlation with food intake and postoperative type 2 diabetes remission (T2Dr). Design: Gut microbiota profile from obese diabetic women was evaluated before (n = 25) and 3 (n = 20) and 12 months (n = 14) after RYGB, using MiSeq Illumina-based V4 bacterial 16S rRNA gene profiling. Data on food intake (7-day record) and T2Dr (American Diabetes Association (ADA) criteria) were recorded. Results: Preoperatively, the abundance of five bacteria genera differed between patients with (57%) and without T2Dr (p < 0.050). Preoperative gut bacteria genus signature was able to predict the T2Dr status with 0.94 accuracy ROC curve (receiver operating characteristic curve). Postoperatively (vs. preoperative), the relative abundance of some gut bacteria genera changed, the gut microbial richness increased, and the Firmicutes to Bacteroidetes ratio (rFB) decreased (p < 0.05) regardless of T2Dr. Richness levels was correlated with dietary profile pre and postoperatively, mainly displaying positive and inverse correlations with fiber and lipid intakes, respectively (p < 0.05). Conclusions: Gut microbiota profile was influenced by RYGB and correlated with diet and T2Dr preoperatively, suggesting the possibility to assess its composition to predict postoperative T2Dr.

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