scholarly journals Diet Rather than Genetic Status Shapes the Gut Microbiota in Two Congeneric Snakes

Author(s):  
Yan-Fu Qu ◽  
Yan-Qing Wu ◽  
Yi-Jin Jiang ◽  
Xiang Ji

Abstract Background: Various external and internal factors affect the gut microbiota of animals. The colonization and proliferation of gut microbes have been studied in a diverse array of animal taxa but remain poorly known in snakes. Here, we used the 16S rRNA gene sequencing technology on the Roach 454 platform to analyze the gut microbiota composition using fecal samples collected from three snake groups [gravid females, newly hatched (preprandial) hatchlings and postprandial hatchlings] of two congeneric colubrid snake species (Elaphe carinata and E. taeniura) that are sympatric across a wide range in mainland China. We tested two hypotheses. First, the gut microbiota should not differ between the two species at hatching if the maternal or genetic contribution has no role in affecting post-hatching gut microbial colonization. Second, differences in the gut microbiota between newly hatched (preprandial) and postprandial hatchlings should not exist in both species if the dietary contribution has no role in affecting post-hatching gut microbial colonization.Results: The top three dominant phyla were Firmicutes, Bacteroidetes, and Proteobacteria in both species. None of the measured alpha diversity indexes differed among the three snake groups or between the two species. The relative abundance of the gut microbiota differed among the three snake groups and between the two species, and so did the relative abundances of the functions associated with the metabolism, cellular processes and environmental information processing. Evidence from gravid females and hatchlings showed that the gut microbiota composition was similar between the two species. The metabolism held the overwhelming predominance of functional categories at the top level in both species.Conclusion: Only the relative abundance of the gut microbiota differed between the two species, and the gut microbiota composition changed rapidly in postprandial hatchlings and differed among the three snakes groups in both species. From these findings, we may conclude that the dietary rather than the maternal or genetic contribution affects gut microbial colonization in snakes.

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Mei Wang ◽  
Brooke Smith ◽  
Brock Adams ◽  
Miller Tran ◽  
Ryan Dilger ◽  
...  

Abstract Objectives Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrhea in human infants and young farm animals. Osteopontin (OPN), a glycoprotein present in high concentration in human milk, has immunomodulatory functions, which could indirectly impact the microbiota. Furthermore, a previous study has shown fecal microbiota composition differs between wild-type and OPN knockout mice. Herein, the effects of OPN-enriched algae on the gut microbiota composition and volatile fatty acid (VFA) concentrations of ETEC-infected piglets were assessed. Methods Naturally-farrowed piglets were sow-reared for 21 days and then randomized to two weaning diets: WT (formula + 1% wild-type algae) or OPN (formula + 1% OPN-enriched algae). On postnatal day (PND) 31, all piglets were infected orally with a live culture of ETEC (1010 colony-forming unit/3 mL dose) daily for three consecutive days. On PND 41, ascending colon (AC) contents were collected. Gut microbiota was assessed by sequencing V3-V4 regions of 16S rRNA gene and VFAs were determined by gas chromatography. Alpha-diversity and VFAs were analyzed using PROC MIXED procedure of SAS. Beta-diversity was evaluated by permutational multivariate analysis of variance (PERMANOVA) and differential abundance analysis on the bacterial genera was performed using DESeq2 package of R. Results Shannon indices were lower in the AC contents of OPN piglets compared to WT piglets. The overall colonic microbiota of OPN piglets differed from that of WT piglets (PERMANOVA P = 0.015). At genus level, OPN-enriched algae increased the abundance of Streptococcus, decreased the abundances of Sutterella, Candidatus Soleaferrea, dga-11 gut group, Rikenellaceae RC9 gut group, Ruminococcaceae UCG-010, unculturedRuminococcaceae, Prevotella 2 and 7 compared to piglets consuming wild-type algae (P < 0. 05). OPN piglets also had higher (P < 0.05) concentrations of acetate, propionate, butyrate and valerate compared to WT. Conclusions In ETEC infected piglets, 1% OPN-enriched algae decreased alpha-diversity and modulated the microbiota composition and VFA profiles compared to 1% WT algae. Other studies have shown that OPN inhibits biofilm formation in vitro, but future research is needed to assess in vivo microbiome-modulation mechanisms. Funding Sources Triton Algae Innovations.


2020 ◽  
Author(s):  
Dandan Jiang ◽  
Xin He ◽  
Marc Valitutto ◽  
Li Chen ◽  
Qin Xu ◽  
...  

Abstract Background:The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains of southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations of metabolite types and bacterial genus were detected. Conclusions: There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.


PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245399
Author(s):  
Ingrid S. Surono ◽  
Dian Widiyanti ◽  
Pratiwi D. Kusumo ◽  
Koen Venema

The gut microbiota has been shown to play a role in energy metabolism of the host. Dysbiosis of the gut microbiota may predispose to obesity on the one hand, and stunting on the other. The aim of the study was to study the difference in gut microbiota composition of stunted Indonesian children and children of normal nutritional status between 3 and 5 years. Fecal samples and anthropometric measurements, in addition to economic and hygiene status were collected from 78 stunted children and 53 children with normal nutritional status in two regions in Banten and West Java provinces: Pandeglang and Sumedang, respectively. The gut microbiota composition was determined by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. The composition was correlated to nutritional status and anthropometric parameters. Macronutrient intake was on average lower in stunted children, while energy-loss in the form of short-chain fatty acids (SCFA) and branched-chain fatty acids (BCFA) appeared to be higher in stunted children. In stunted children, at the phylum level the relative abundance of Bacteroidetes (44.4%) was significantly lower than in normal children (51.3%; p-value 2.55*10−4), while Firmicutes was significantly higher (45.7% vs. 39.8%; p-value 5.89*10−4). At the genus level, overall Prevotella 9 was the most abundant genus (average of 27%), and it was significantly lower in stunted children than in normal children (23.5% vs. 30.5%, respectively; q-value 0.059). Thirteen other genera were significantly different between stunted and normal children (q-value < 0.1), some of which were at low relative abundance and present in only a few children. Prevotella 9 positively correlated with height (in line with its higher relative abundance in normal children) and weight. In conclusion, Prevotella 9, which was the most abundant genus in the children, was significantly lower in stunted children. The abundance of Prevotella has been correlated with dietary fibre intake, which was lower in these stunted children. Since fibres are fermented by the gut microbiota into SCFA, and these SCFA are a source of energy for the host, increasing the proportion of Prevotella in stunted children may be of benefit. Whether this would prevent the occurrence of stunting or even has the potential to revert it, remains to be seen in follow up research.


2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Dandan Jiang ◽  
Xin He ◽  
Marc Valitutto ◽  
Li Chen ◽  
Qin Xu ◽  
...  

Abstract Background The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains in southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. Results The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations between metabolite types and bacterial genus were detected. Conclusions There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.


2019 ◽  
Vol 10 (3) ◽  
pp. 253-263 ◽  
Author(s):  
S. Soldi ◽  
S. Vasileiadis ◽  
S. Lohner ◽  
F. Uggeri ◽  
E. Puglisi ◽  
...  

Supplementing kindergarten children during a cold season with a prebiotic inulin-type fructans product with shorter and longer fructan chains has been shown to reduce febrile episodes requiring medical attention and to lower the incidence of sinusitis. These beneficial effects may be connected to the specific modulation of children’s gut microbiota. By applying quantitative and qualitative microbiota analysis this study aimed at characterising the gut microbiota composition and at exploring effects of prebiotic intervention on the gut microbiota during a 24-weeks intervention and during antibiotic treatment in healthy children. The study was a randomised, placebo-controlled trial with 258 healthy children aged 3 to 6 years consuming 6 g/day prebiotic inulin-type fructans or maltodextrin. During the course of the study, faecal samples were collected and subject to targeted qPCR analysis and phylogenetic profiling by multiplexed high throughput sequencing of the prokaryotic 16S rRNA gene PCR amplicons. The microbiota composition of the cohort could be clustered into three distinct constellations (enterotypes). Prebiotic intake resulted in a selective modulation of the gut microbiota composition. Relative abundance of Bifidobacterium was significantly higher in the prebiotic group (n=104) compared to control group (n=105) and this effect was found for all three enterotypes. Antibiotic administration decreased the relative abundance of Bifidobacterium in both groups. Nonetheless, children of the prebiotic group receiving antibiotic treatment displayed significantly higher levels of Bifidobacterium than children receiving the placebo control. Prebiotic supplementation induced specific changes in the gut microbiota composition of children aged 3 to 6 years. Moreover, it attenuated antibiotic-induced disturbances in the gut microbiota composition as shown by higher relative abundance of bifidobacteria at the end of the antibiotic treatment in the prebiotic group. With the previously reported benefits on immune function, the study contributes to the evidence on the immune-modulating effects of prebiotics through gut microbiota modifications. The study was registered as NCT03241355 ( https://clinicaltrials.gov/show/NCT03241355 ).


2020 ◽  
Vol 8 (5) ◽  
pp. 677 ◽  
Author(s):  
Monique J. T. Crobach ◽  
Quinten R. Ducarmon ◽  
Elisabeth M. Terveer ◽  
Celine Harmanus ◽  
Ingrid M. J. G. Sanders ◽  
...  

Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p < 0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients’ gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.


Nutrients ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2364 ◽  
Author(s):  
Xiaozhong Zhong ◽  
Janas M. Harrington ◽  
Seán R. Millar ◽  
Ivan J. Perry ◽  
Paul W. O’Toole ◽  
...  

Emerging evidence links the gut microbiota with several chronic diseases. However, the relationships between metabolic syndrome (MetS), obesity and the gut microbiome are inconsistent. This study aimed to investigate associations between gut microbiota composition and diversity and metabolic health status in older adults (n = 382; median age = 69.91 [± 5 years], male = 50.79%) with and without obesity. Gut microbiome composition was determined by sequencing 16S rRNA gene amplicons. Results showed that alpha diversity and richness, as indicated by the Chao1 index (p = 0.038), phylogenetic diversity (p = 0.003) and observed species (p = 0.038) were higher among the metabolically healthy non-obese (MHNO) individuals compared to their metabolically unhealthy non-obese (MUNO) counterparts. Beta diversity analysis revealed distinct differences between the MHNO and MUNO individuals on the phylogenetic distance scale (R2 = 0.007, p = 0.004). The main genera contributing to the gut composition among the non-obese individuals were Prevotella, unclassified Lachnospiraceae, and unclassified Ruminococcaceae. Prevotella, Blautia, Bacteroides, and unclassified Ruminococcaceae mainly contributed to the variation among the obese individuals. Co-occurrence network analysis displayed different modules pattern among different metabolic groups and revealed groups of microbes significantly correlated with individual metabolic health markers. These findings confirm relationships between metabolic health status and gut microbiota composition particularly, among non-obese older adults.


Nutrients ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2308
Author(s):  
Annefleur M. Koopen ◽  
Nicolien C. de Clercq ◽  
Moritz V. Warmbrunn ◽  
Hilde Herrema ◽  
Mark Davids ◽  
...  

Plasma metabolites affect a range of metabolic functions in humans, including insulin sensitivity (IS). A subset of these plasma metabolites is modified by the gut microbiota. To identify potential microbial–metabolite pathways involved in IS, we investigated the link between plasma metabolites, gut microbiota composition, and IS, using the gold-standard for peripheral and hepatic IS measurement in a group of participants with metabolic syndrome (MetSyn). In a cross-sectional study with 115 MetSyn participants, fasting plasma samples were collected for untargeted metabolomics analysis and fecal samples for 16S rRNA gene amplicon sequencing. A two-step hyperinsulinemic euglycemic clamp was performed to assess peripheral and hepatic IS. Collected data were integrated and potential interdependence between metabolites, gut microbiota, and IS was analyzed using machine learning prediction models. Plasma metabolites explained 13.2% and 16.7% of variance in peripheral and hepatic IS, respectively. Fecal microbiota composition explained 4.2% of variance in peripheral IS and was not related to hepatic IS. Although metabolites could partially explain the variances in IS, the top metabolites related to peripheral and hepatic IS did not significantly correlate with gut microbiota composition (both on taxonomical level and alpha-diversity). However, all plasma metabolites could explain 18.5% of the variance in microbial alpha-diversity (Shannon); the top 20 metabolites could even explain 44.5% of gut microbial alpha-diversity. In conclusion, plasma metabolites could partially explain the variance in peripheral and hepatic IS; however, these metabolites were not directly linked to the gut microbiota composition, underscoring the intricate relation between plasma metabolites, the gut microbiota, and IS in MetSyn


Toxics ◽  
2022 ◽  
Vol 10 (1) ◽  
pp. 34
Author(s):  
Zhiwei Bao ◽  
Weitao Wang ◽  
Xiaofang Wang ◽  
Mingrong Qian ◽  
Yuanxiang Jin

Difenoconazole (DIF) is a widely separated triazole fungicide in many countries. The excessive usage of DIF increases the high volume of residues in agriculture production and water bodies. Some previous studies demonstrated the toxic effects of DIF on non-target animals, however, there were still some gaps in the knowledge of the potential hazards of DIF to mammals and human health. Herein, 7-week-old male mice were exposed to 30 and 100 mg/kg/day DIF for 14 and 56 days. We observed that 56 days of DIF exposure decreased the colonic mucus expression of alcin blue-periodic acid-schiff (AB-PAS) stain and the immunochemical stain of muc2 protein. The transcript levels of mucin protein (muc1, muc2 and muc3) decreased significantly in the gut of mice followed 56 days of 100 mg/kg/day DIF exposure. In addition, the gut microbiota composition was also affected after 14 or 56 days of DIF exposure. Although the mucus expression after 14 days of DIF exposure only decreased slightly, the gut microbiota composition compared with the control group was changed significantly. Moreover, the DIF-30 and DIF-100 caused respectively different changes on the gut microbiota. The relative abundance of Bacteroidetes decreased significantly after 14 days and 56 days of DIF exposure. After 14 days of DIF exposure, there were 35 and 18 differential genera in the DIF-30 and DIF-100 group, respectively. There were 25 and 32 differential genera in the DIF-30 and DIF-100 group after 56 days of exposure, respectively. Meanwhile, the alpha diversity indexes, including observed species, Shannon, Simpson, Chao1 and ACE, in gut microbiota decreased significantly after 56 days of DIF exposure. Interestingly, the relative abundance of Akkermansia increased significantly after 56 days of 100 mg/kg/d DIF exposure. Although Akkermansia was considered as one probiotic, the phenomenon of dramatic Akkermansia increase with the decrease in gut microbiota diversity needed further discussion. These results provided some new insights on how DIF exposure impacts the mucus barrier and induces gut microbiota dysbiosis.


2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 378-378
Author(s):  
Mei Wang ◽  
Marcia Monaco ◽  
Victoria C Daniels ◽  
Johanna Hirvonen ◽  
Henrik Max Jensen ◽  
...  

Abstract Objectives Human milk is a source of oligosaccharides that promote the growth of beneficial bacteria. Bifidobacterium longum subsp. infantis, a dominant species in breastfed infants, has the capacity to utilize milk oligosaccharides. Herein, the effects of 2'fucosyllactose (2'FL), B. infantis Bi-26 (Bi-26), and a combination thereof on piglet gut microbiota composition and volatile fatty acid (VFA) concentrations were assessed. Methods Fifty-two intact male pigs were provided ad libitum access to a nutritionally-adequate milk replacer without (CON) or with 1.0 g/L 2’FL (FL) from postnatal day 2 to 34/35. Pigs were further stratified to receive either 12% glycerol or Bi-26 in glycerol orally, 109 colony-forming unit/day (BI and FLBI). Ascending colon (AC) and rectal contents were collected. Gut microbiota profiles were assessed by 16S rRNA gene sequencing and real-time PCR and VFA were determined by gas chromatography. Results Neither 2'FL nor Bi-26 affected the overall microbiota composition (P &gt; 0. 05); however, alpha diversity and the relative abundances of bacterial genera were influenced by the treatments. Shannon indices were lower in AC of piglets fed Bi-26 (P = 0.048). Proportions of Clostridia UCG-014, Lachnoclostridium, Christensenellaceae R-7 group and Anaerovoracaceae family XIII AD3011 group were lower, while Faecalibacterium was higher in AC of piglets receiving 2'FL (P &lt; 0.05). Bi-26 decreased (P &lt; 0.05) colonic abundances of Parabacteroides, Fusobacterium, Butyricimonas and uncultured Prevotellaceae. In rectal contents,7 bacterial genera were impacted by 2'FL and 3 by Bi-26 (P &lt; 0.05). Interactive effects were observed for several bacterial genera and acetate concentrations (P &lt; 0.05). In AC, Lachnospiraceae CAG-56 was higher in CON than all other groups and Allisonella was lower in BI piglets vs. CON. Rectal contents Bacteroides was higher in BI piglets than CON. Compared to CON, acetate concentrations were higher in AC of FL piglets (P &lt; 0.05). Conclusions 2'FL and Bi-26 supplemented to milk replacer exerted individual and synbiotic influences on gut bacterial composition, and 2'FL alone increased specific VFA concentration, demonstrating its prebiotic potential. Funding Sources DuPont Nutrition and Biosciences.


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