scholarly journals The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wen Wang ◽  
Xiaolong Gao ◽  
Sisi Zheng ◽  
Zhuoma Lancuo ◽  
Ying Li ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Pathogenic Bacteria ◽  
Feeding Habits ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Diversity ◽  
Protective Role ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Beneficial Bacteria ◽  
Fecal Samples

Abstract Background Himalayan Griffons (Gyps himalayensis), large scavenging raptors widely distributed in Qinghai-Tibetan Plateau, have evolved a remarkable ability to feed on carcasses without suffering any adverse effects. The gut microbiome plays an important role in animal physiological and pathological processes, and has also been found to play a health protective role in the vulture adaptation to scavenging. However, the microbial taxonomic diversity (including nonculturable and culturable microbes), functions, and metabolites related to Himalayan Griffons have not been fully explored. Methods In the present study, the 28 fecal samples of the Himalayan Griffons and 8 carrion samples were collected and sequenced using high-throughput 16S rRNA gene sequencing methods to analyze the composition and functional structures of the microbiomes. Twelve fecal samples of the Himalayan Griffons were analyzed using untargeted Liquid Chromatography Mass Spectroscopy (LC–MS) to identify metabolites. We used different culture conditions to grow Himalayan Griffons gut microbes. Inhibitory effects of gut beneficial bacteria on 5 common pathogenic bacteria were also tested using the Oxford cup method. Results According to the results of the culture-independent method, a high abundance of four major phyla in Himalayan Griffons were identified, including Fusobacteria, Firmicutes, Bacteroidetes, and Proteobacteria. The most abundant genera were Fusobacterium, followed by Clostridium_sensu_stricto_1, Cetobacterium, Epulopiscium, and Bacteroides. The predicted primary functional categories of the Himalayan Griffons’ gut microbiome were associated with carbohydrate and amino acid metabolism, replication and repair, and membrane transport. LC–MS metabolomic analysis showed a total of 154 metabolites in all the fecal samples. Cultivation yielded 184 bacterial isolates with Escherichia coli, Enterococcus faecium, Enterococcus hirae, and Paeniclostridium sordellii as most common isolates. Moreover, 7 potential beneficial gut bacteria isolated showed certain inhibition to 5 common pathogenic bacteria. Conclusions Our findings broaden and deepen the understanding of Himalayan Griffons’ gut microbiome, and highlighted the importance of gut microbiome-mediated adaptation to scavenging habits. In particular, our results highlighted the protective role of gut beneficial bacteria in the Himalayan Griffons against pathogenic bacteria that appear in rotten food resources.

scholarly journals PSII-24 Towards a better understanding of the gut microbiome functions in the swine production: extensive cultivation of the swine gut microbiome from different growth stages

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 242-243
Author(s):  
Xiaofan Wang ◽  
Xiaoyuan Wei ◽  
Feilong Deng ◽  
Tsungcheng Tsai ◽  
Charles V Maxwell ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Pathogenic Bacteria ◽  
Illumina Miseq ◽  
Positive Control ◽  
Growth Stages ◽  
Rrna Gene ◽  
Swine Production ◽  
Fecal Samples ◽  
Different Growth Stages

Abstract Substantial progress has been made in the culture-omics of the human gut microbiota. However, little is known about the culture-omics of the swine gut microbiota, despite recent reports of their significant roles in swine health and production. To fill this knowledge gap in research, we tested 52 bacterial cultivation methods with different media and gas combinations. Fresh fecal samples (0.2g/sample) were collected from three pigs at the end of four growth stages: lactation, nursery, growing and finishing and were mixed with a stomacher in 20 mL saline. Aliquots of 50 uL microbial suspensions were then spread onto different media plates and incubated under aerobic and anaerobic conditions at 37C for up to 5 days. An additional aliquot of each sample was subjected to direct DNA extraction as a positive control. Bacterial colonies from each plate were collected and DNA was extracted from these samples using the Powersoil DNA isolation kit and sequenced with an Illumina Miseq sequencer targeting the V4 region of the 16S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. A total of 378, 482, 565, and 555 bacterial features were observed from microbial solutions at the end of lactation, nursery, growing and finishing. Our culturing methods recovered 415, 675, 808, and 823 features correspondingly, representing 45.2%, 54.8%, 53.3%, and 56.4% of total features observed in microbial solutions. The top ten most easily cultured genus were Escherichia, Streptococcus, Lactobacillus, Megasphaera, Acidaminococcus, Bacillus, Mitsuokella, Enterococcus and Prevotella. Non-parametric permutational multivariate analysis of variance shows that the main factors driving the swine culture-omics included medium, age and oxygen condition. This study identifies the cultivable bacteria from fecal samples collected at different growth stages of pigs and provides a guidance to cultivate potential beneficial or pathogenic bacteria of interests and validate their functions in swine production.

scholarly journals A case–control study on the association of intestinal flora with ulcerative colitis

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yin-hua Tang ◽  
Hong-cheng Liu ◽  
Guang Song ◽  
Tian-tian Wu ◽  
Ying Zhao ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Pathogenic Bacteria ◽  
Intestinal Flora ◽  
16S Rrna Gene Sequencing ◽  
Control Group ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Fecal Samples ◽  
Healthy Control ◽  
Rrna Gene Sequencing

AbstractThe association between intestinal flora and ulcerative colitis (UC) was studied in order to provide a basis and method for clinical treatment. Fresh fecal samples were collected from 30 active UC patients and 10 healthy controls. The intestinal flora DNA from each sample was extracted and 16S rRNA gene sequencing was carried out using HiSeq platform to identify the intestinal flora in fecal samples. The richness and diversity of intestinal flora in UC patients were significantly lower than those in healthy control group (P < 0.05). Significant differences were observed between the intestinal flora-species of UC patients and healthy controls. Synergistetes (P < 0.01) and Firmicutes (P < 0.05), along with probiotics Veillonella (P < 0.01), Ruminococcus and Coprococcus (P < 0.05) in the UC patients were lower than that in the healthy controls significantly. Furthermore, compared with the control group, Tenericutes (P < 0.01) and intestinal pathogenic bacteria, including Bacteroides (P < 0.01), Escherichia and Sutterella (P < 0.05) were significantly increased. The incidence of UC is significantly associated with the changes in intestinal flora. Changes in intestinal flora may lead to a decrease in the diversity of intestinal flora or to the enrichment of a particular intestinal flora.

scholarly journals Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Esteban Góngora ◽  
Kyle H. Elliott ◽  
Lyle Whyte
Keyword(s):  
Gut Microbiome ◽  
Sulfur Isotopes ◽  
Trophic Position ◽  
Isotope Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Uria Lomvia ◽  
Fecal Microbiome ◽  
Prey Specialization ◽  
Rrna Gene Sequencing

AbstractThe role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

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

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.

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

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.

scholarly journals The Diversity of the Intestinal Flora Disturbed After Feeding Intolerance Recovery in Preterm Twins

2021 ◽  
Vol 9 ◽  
Author(s):  
Ying Li ◽  
Chunhong Jia ◽  
Xiaojun Lin ◽  
Lili Lin ◽  
Lizhen Li ◽  
...  
Keyword(s):  
Acid Metabolism ◽  
Intestinal Flora ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Feeding Intolerance ◽  
Fecal Samples ◽  
Kegg Pathways ◽  
Intestinal Bacterial Community ◽  
Β Diversity ◽  
Significant Difference

Background: Feeding intolerance (FI) is a common condition in premature infants that results in growth retardation and even necrotizing enterocolitis. The gut microbiome is linked to FI occurrence; however, the outcome after FI recovery is unclear.Methods: Fecal samples were collected from 11 pairs of premature twins/triplets for 16S rRNA gene sequencing. Initial fecal samples were collected shortly after admission, and then every other week until 7 weeks or discharge.Results: After FI recovery, there was no significant difference in the β-diversity of the intestinal flora between the FI group and the feeding tolerance (FT) group. By contrast, there was a significant difference in the β-diversity. Proteobacteria was the predominant phylum in the microbiome of the FI group, whereas Firmicutes was the predominant phylum in the microbiome of the FT group. The predominant bacteria with LDA &gt;4 between the two groups at 13–15 days after birth, 19–28 days after birth, and at discharge were different, with the proportions of Bacillus, Clostridium butyricum, and Clostridium being highest in the FT group and Firmicutes, unidentified_Clostridiales, and Proteobacteria being highest in the FI group. Similarly, there were significant differences in the relative abundances of KEGG pathways, such as fatty acid metabolism, DNA repair and recombination proteins, energy metabolism, and amino acid metabolism, between the two groups (P &lt; 0.01).Conclusions: There was a significant difference in diversity of the intestinal flora after feeding intolerance recovery. Feeding intolerance may disturb the succession of the intestinal bacterial community.

scholarly journals A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility

2020 ◽  
Author(s):  
Blake W. Stamps ◽  
Wanda J. Lyon ◽  
Adam P. Irvin ◽  
Nancy Kelley-Loughnane ◽  
Michael S. Goodson
Keyword(s):  
Pilot Study ◽  
16S Rrna ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Initial Study ◽  
Mitigation Strategies ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Traveler’S Diarrhea ◽  
Traveler's Diarrhea

AbstractTraveler’s diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers’ diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to traveler’s diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.

scholarly journals The Effect of White Rice and White Bread as Staple Foods on Gut Microbiota and Host Metabolism

Nutrients ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 1323 ◽  
Author(s):  
Fumika Mano ◽  
Kaori Ikeda ◽  
Erina Joo ◽  
Yoshihito Fujita ◽  
Shunsuke Yamane ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Intervention ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
White Bread ◽  
Fecal Samples ◽  
White Rice ◽  
Staple Foods ◽  
Glucagon Like Peptide 1 ◽  
Side Dishes

The purpose of this study was to examine the influence of two kinds of major Japanese staple foods, white rice and white bread, on gut microbiota against the background in which participants eat common side dishes. Seven healthy subjects completed the dietary intervention with two 1-week test periods with a 1-week wash-out period in cross-over design (UMIN registration UMIN000023142). White bread or white rice and 21 frozen prepared side dishes were consumed during the test periods. At baseline and at the end of each period, fasting blood samples, breath samples, and fecal samples were collected. For fecal samples, 16S rRNA gene sequencing was used to analyze the gut microbiota. After the bread period, the abundance of fecal Bifidobacterium genus (19.2 ± 14.5 vs. 6.2 ± 6.6 (%), p = 0.03), fasting glucagon-like peptide 1 (GLP-1) (13.6 ± 2.0 vs. 10.5 ± 2.9 (pg/mL), p = 0.03), and breath hydrogen (23.4 ± 9.9 vs. 8.2 ± 5.5 (ppm), p = 0.02) were significantly higher than those of after the rice period. Plasma SCFAs also tended to be higher after the bread period. White bread contains more dietary fiber than refined short grain rice. These findings suggest that indigestible carbohydrate intake from short grain rice as a staple food may be smaller than that of white bread.

199 Do the Microbiomes of Horses Process Nutrients Differently Based on Keeper Status?

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 106-106
Author(s):  
Alexa C Johnson ◽  
Amy S Biddle
Keyword(s):  
Fixed Effects ◽  
High Performance ◽  
16S Rrna Gene Sequencing ◽  
Gas Production ◽  
Rrna Gene ◽  
Total N ◽  
Fermentation Products ◽  
Fecal Samples ◽  
Α Diversity ◽  
C 50

Abstract This study reports the differential response of the equine gut microbiome to protein and/or carbohydrate based on keeper status (easy keeper (EK), medium keeper (MK), hard keeper (HK)). Anaerobic equine fecal samples (n = 12 total, n = 3 / EK, MK, HK of four breeds) inoculated microcosms with three dietary conditions (C = Carb (cornmeal), P = Protein (soybean meal), and M = mix (50% C, 50% P)). Over 48 hours, fermentation products were measured using colorimetric assays and high-performance liquid chromatography. Microbial populations were surveyed using 16S rRNA gene sequencing analyzed by QIIME2. Linear mixed models were fit with fixed effects of Treatment and Keeper status and their interactions, with random effects of HorseID. Differences in fermentation products by keeper status included: MK had higher pH and greater gas production, EK produced higher hydrogen sulfide, and HK had greater total protein. Total SCFA was not different between keeper status (P = 0.89) but the acetate: propionate ratio was highest for HK (2.45mM) and lowest for EK (1.85mM) (P = 0.05). Isobutyrate production was highest in HK (2.34mM) compared to MK (0.85mM) and EK (0.17mM). Treatment had significant effects across all measurements; M and C treatment values were similar reflecting microbial preferences for carbohydrates before protein. P treated trials had increased fermentation outputs due to lower acidity effects. Keeper status had no effect on α-diversity (P &gt; 0.05) however HK horses were least affected by treatments. P treated samples were more diverse than C and M (P &lt; 0.001). Spearman correlation of Keeper x Treatment identified Oligosphaeria spp. in EK (r = 0.49) and Fusobacteria spp. in HK whole fecal samples (r = 0.37). These data suggest that while the compositions of the gut microbiomes of keeper groups were similar, they were functionally different in processing key nutrients.

Abstract 18: Gut Microbiome Modifies the Protective Effects of a Mediterranean Dietary Pattern Against Diabetes Mellitus in US Hispanics/ Latinos: The Hispanic Community Health Study/ Study of Latinos (HCHS/SOL)

Circulation ◽  
2020 ◽  
Vol 141 (Suppl_1) ◽  
Author(s):  
Dong Wang ◽  
Qibin Qi ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Health Study ◽  
Rrna Gene ◽  
Inverse Association ◽  
Protective Effects ◽  
Acid Fermentation ◽  
Microbiome Composition

Introduction: Little is known about whether the effect of a healthy diet on diabetes mellitus (DM) is modified by the gut microbiome in human. Hypothesis: We hypothesize that the gut microbiome modifies the inverse association between the Mediterranean diet (MedDiet) and risk of DM. Methods: This study included 543 DM cases, 805 with impaired glucose tolerance (IGT) and 394 with normal glucose regulation (NGR) in adults 23-83yrs old from the HCHS/SOL. Fecal samples were profiled using 16s rRNA gene sequencing. We applied QIIME 2 to cluster sequences into OTUs and assign taxonomies, and PICRUSt to predict metagenomic gene functions. Adherence to the MedDiet was evaluated by a MedDiet index using the average of two 24-hr dietary recalls. We applied MaAsLin2 to quantify associations between the MedDiet index and microbial features with adjustment for confounding factors listed in the caption of Fig. 1. Results: MedDiet was associated with phylogenetically diverse, rare, and abundant gut microbes (Fig. 1a). For example, a higher MedDiet index was associated with a higher relative abundance of Faecalibacterium Prausnitzii [FDR-adjusted p (q) =0.002], but a lower relative abundance of Collinsella aerofaciens ( q =0.009). We found that several microbial functions related to plant-derived polysaccharide degradation such as fructuronate reductase ( q =0.02), and short-chain fatty acid fermentation such as butyryl-CoA dehydrogenase ( q =0.002) were enriched in participants with higher MedDiet index. We found that the inverse association between MedDiet and risk of DM was more pronounced in participants with greater abundance of Prevotella copri , but weaker in participants whose gut microbial communities were dominated by Bacteroides ( P interaction =0.02 for IGT/DM vs NGR, Fig. 1b). Conclusions: Adherence to the MedDiet is associated with diverse gut microorganisms and microbial functions. The inverse association between MedDiet and risk of DM might be modified by gut microbiome composition. 1

Sign in / Sign up

Export Citation Format

Share Document