scholarly journals Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found

2021 ◽  
Vol 9 (2) ◽  
pp. 391
Author(s):  
Shyam Sundar Paul ◽  
Rudra Nath Chatterjee ◽  
Mantena Venkata Lakshmi Narasimha Raju ◽  
Bhukya Prakash ◽  
Savaram Venkata Rama Rao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Microbial Composition ◽  
Linear Discriminant ◽  
Specific Complex ◽  
Commercial Broiler ◽  
16S Rdna Amplicon Sequencing ◽  
Chicken Breeds ◽  
And Performance

Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we characterized the gut microbiota of “finishing” chickens (at the end of production life) of indigenous Indian Nicobari, Ghagus, and Aseel breeds, originating from the Nicobari island, coastal India, and the Indian mainland, respectively, as well as a global commercial broiler line, VenCobb 400, using 16S rDNA amplicon sequencing. We found that diversity, as well as richness of microbiota, was higher in indigenous breeds than in the broiler line. Beta diversity analysis indicated the highest overlap between Ghagus and Nicobari breeds and a very low overlap between the broiler line and all indigenous breeds. Linear discriminant analysis effect size (LEfSe) revealed 82 breed- or line-specific phylotype operational taxonomic unit (OTU) level biomarkers. We confirm the presence of breed specific and across-breed core microbiomes. Additionally, we show the existence of breed specific complex microbial networks in all groups. This study provides the first (and comprehensive) insight into the gut microbiota of three indigenous breeds and one commercial broiler line of chickens reared without antimicrobials, and underscores the need to study microbial diversity in other indigenous breeds.

scholarly journals Alterations in The Gut Microbiota and Metabolite Profiles in The Context of Neuropathic Pain

2021 ◽  
Author(s):  
Peng Chen ◽  
Chen Wang ◽  
Yan-na Ren ◽  
Zeng-jie Ye ◽  
Chao Jiang ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Neuropathic Pain ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Differentially Expressed ◽  
Metabolic Disturbances ◽  
Serum Metabolites ◽  
Genus Level ◽  
Metabolite Profiles ◽  
16S Rdna Amplicon Sequencing

Abstract The aim of this study was to explore the relationships among gut microbiota disturbances and serum and spinal cord metabolic disorders in neuropathic pain. 16S rDNA amplicon sequencing and serum and spinal cord metabolomics were used to identify alterations in the microbiota and metabolite profiles in the sham rats and the chronic constriction injury (CCI) model rats. Correlations between the abundances of gut microbiota components at the genus level, the levels of serum metabolites, and pain-related behavioural parameters were analysed. Ingenuity pathway analysis (IPA) was applied to analyse the interaction networks of the differentially expressed serum metabolites. First, we found that the composition of the gut microbiota was different between rats with CCI-induced neuropathic pain and sham controls. At the genus level, the abundances of Helicobacter, Phascolarctobacterium, Christensenella, Blautia, Streptococcus, Rothia and Lactobacillus were significantly increased, whereas the abundances of Ignatzschineria, Butyricimonas, Escherichia, AF12, and Corynebacterium were significantly decreased. Additionally, 72 significantly differentially expressed serum metabolites and 17 significantly differentially expressed spinal cord metabolites were identified between the CCI rats and the sham rats. Finally, correlation analysis showed that changes in the gut microbiota was significantly correlated with changes in serum metabolite levels, suggesting that dysbiosis of the gut microbiota is an important factor in modulating metabolic disturbances in the context of neuropathic pain. In conclusion, our research provides a novel perspective on the potential roles of the gut microbiota and related metabolites in neuropathic pain.

scholarly journals Pyruvate Might Bridge Gut Microbiota and Muscle Health in Aging Mice After Chronic High Dose of Leucine Supplementation

2021 ◽  
Vol 8 ◽  
Author(s):  
Yuxiao Liao ◽  
Dan Li ◽  
Xiaolei Zhou ◽  
Zhao Peng ◽  
Zitong Meng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Ultrasound Measurement ◽  
High Dose ◽  
Leucine Supplementation ◽  
Cross Sectional ◽  
Pyruvate Fermentation ◽  
Before And After ◽  
16S Rdna Amplicon Sequencing ◽  
Muscle Health

Background: The previous studies demonstrated that there might be complex and close relationships among leucine supplementation, gut microbiota, and muscle health, which still needs further investigation.Aims: This study aimed to explore the associations of gut microbiota with muscle health after leucine intake.Methods: In this study, 19-month-old male C57BL/6j mice (n = 12/group) were supplemented with ultrapure water, low dose of leucine (500 mg/kg·d), and high dose of leucine (1,250 mg/kg·d) for 12 weeks by oral gavage. The mice fecal samples in each group before and after supplementation were collected for baseline and endpoint gut microbiota analysis by using 16S rDNA amplicon sequencing. Meanwhile, ultrasound measurement, H&E staining, myofiber cross-sectional area (CSA) measurement, and western blotting were performed in the quadriceps subsequently. The pyruvate levels were detected in feces.Results: Improvement in muscle of histology and ultrasonography were observed after both low and high dose of leucine supplementation. High dose of leucine supplementation could promote skeletal muscle health in aging mice via regulating AMPKα/SIRT1/PGC-1α. The richness and diversities of microbiota as well as enriched metabolic pathways were altered after leucine supplementation. Firmicutes-Bacteroidetes ratio was significantly decreased in high-leucine group. Moreover, pyruvate fermentation to propanoate I were negatively associated with differential species and the pyruvate levels were significantly increased in feces after high dose of leucine supplementation.Conclusions: Chronic high dose of leucine supplementation changed gut microbiota composition and increased pyruvate levels in the feces, which possibly provides a novel direction for promoting muscle health in aging mice.

scholarly journals Electroacupuncture could balance the gut microbiota and improve the learning and memory abilities of Alzheimer’s disease animal model

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259530
Author(s):  
Jing Jiang ◽  
Hao Liu ◽  
Zidong Wang ◽  
Huiling Tian ◽  
Shun Wang ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Animal Model ◽  
Gut Microbiota ◽  
Learning And Memory ◽  
Amplicon Sequencing ◽  
Tnf Α ◽  
16S Rdna Amplicon Sequencing ◽  
Nerve System ◽  
Samp8 Mice

Alzheimer’s disease (AD), as one of most common dementia, mainly affects older people from the worldwide. In this study, we intended to explore the possible mechanism of improving cognitive function and protecting the neuron effect by electroacupuncture. Method: We applied senescence-accelerated mouse prone 8 (SAMP8) mice as AD animal model, used Morris water maze, HE staining, 16S rDNA amplicon sequencing of gut microbiota and ELISA to demonstrate our hypothesis. Results: electroacupuncture improved the learning and memory abilities in SAMP8 mice (P<0.05) and could protect the frontal lobe cortex and hippocampus of SAMP8 mice; electroacupuncture significantly decreased the expression of IL-1β (P<0.01), IL-6 (P<0.01) and TNF-α (P<0.01 in hippocampus, P<0.05 in serum) in serum and hippocampus; electroacupuncture balanced the quantity and composition of gut microbiome, especially of the relative abundance in Delta-proteobacteria (P<0.05) and Epsilon-proteobacteria (P<0.05). Conclusion: electroacupuncture treatment could inhibit the peripheral and central nerve system inflammatory response by balancing the gut microbiota.

A Comparative Study of the Gut Microbiota Associated with Immunoglobulin A Nephropathy and Membranous Nephropathy

2020 ◽  
Author(s):  
shiren sun ◽  
Ruijuan Dong ◽  
Ming Bai ◽  
Jin Zhao ◽  
Di Wang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Membranous Nephropathy ◽  
Kidney Biopsy ◽  
Immunoglobulin A ◽  
Amplicon Sequencing ◽  
Healthy Controls ◽  
Immunoglobulin A Nephropathy ◽  
Positive Correlation ◽  
16S Rdna Amplicon Sequencing ◽  
The Oxford Classification

Abstract Background The pathogenesis of immunoglobulin A nephropathy (IgAN) and membranous nephropathy (MN) is characterized by immune dysregulation, which is related to gut dysbiosis. The aim of the study was to compare the gut microbiota of patients with IgAN and MN versus healthy controls. We used 16S rDNA amplicon sequencing to investigate the bacterial communities of 44 patients with kidney biopsy-proven IgAN, 40 patients with kidney biopsy-proven MN, and 30 matched healthy controls (HC). Results The abundance of Escherichia-Shigella and Defluviitaleaceae_incertae_sedis were significantly higher in IgAN than in HC, whereas lower abundances were observed for Roseburia, Lachnospiraceae_ unclassified, Clostridium_sensu_stricto_1, and Fusobacterium . Furthermore, the abundance of Escherichia-Shigella, Peptostreptococcaceae_incertae_sedis , Streptococcus, and Enterobacteriaceae_ unclassified increased, while that of Lachnospira, Lachnospiraceae_ unclassified, Clostridium_sensu_stricto_1, and Veillonella decreased in MN. The abundance of Megasphaera and Bilophila was higher, whereas that of Megamonas, Veillonella, Klebsiella, and Streptococcus was lower in patients with IgAN than in those with MN. Analysis of the correlations showed that in the IgAN group, Prevotella was positively correlated, while Klebsiella , Citrobacter, and Fusobacterium were negatively correlated with the level of serum albumin. Positive correlation also existed between Bilophila and Crescents in the Oxford classification of IgAN. In the MN group, negative correlation was observed between Escherichia-Shigella and proteinuria, Bacteroides and Klebsiella showed positive correlation with the MN stage. Conclusions Patients with IgAN and MN exhibited gut microbial signatures distinct from healthy controls. Our study suggests the potential of gut microbiota as specific biomarker and contributor in the pathogenesis of IgAN and MN.

scholarly journals Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene

2021 ◽  
Vol 9 (4) ◽  
pp. 751
Author(s):  
Jiangwei Li ◽  
Anyi Hu ◽  
Shijie Bai ◽  
Xiaoyong Yang ◽  
Qian Sun ◽  
...  
Keyword(s):  
Community Assembly ◽  
Reductive Dechlorination ◽  
Amplicon Sequencing ◽  
Underlying Mechanism ◽  
Contaminated Sites ◽  
Bioinformatics Analyses ◽  
16S Rdna Amplicon Sequencing ◽  
And Performance ◽  
Stochastic Forces ◽  
Anaerobic Media

Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.

scholarly journals Physical activity and gut microbiota: a cross-sectional study

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
F Gallè ◽  
F Valeriani ◽  
M Antinozzi ◽  
R Liguori ◽  
G Gianfranceschi ◽  
...  
Keyword(s):  
Physical Activity ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Cross Sectional Study ◽  
Microbiota Composition ◽  
Sectional Study ◽  
Microbial Composition ◽  
Cross Sectional ◽  
Bacterial Phyla ◽  
Gut Microbiota Composition

Abstract Background The composition of gut microbiota, and in particular the intestinal abundance of the two main bacterial phyla of Firmicutes and Bacteroidetes, are associated with human health and diseases and may be conditioned by host and environmental factors such as age, gender and diet. The role of Physical Activity (PA) in determining gut microbiota composition has not been yet completely clarified. A cross-sectional study involving undergraduates from two Italian cities is ongoing to explore this relationship. Methods Students were invited to provide a fecal sample and to complete the International Physical Activity Questionnaire (IPAQ) in order to define their habitual PA level (inactive, minimally active, health enhancing physical activity -HEPA- active). Demographic and anthropometric information were also collected. DNA from fecal samples was analyzed through the 16S amplicon sequencing. Microbial composition and variability of the samples were evaluated on the light of participants' PA levels. Results A total of 153 students (47.7% males, mean age 22.4±2.9, mean BMI 22.3±2.7) participated to the study so far. Firmicutes and Bacteroidetes were the main represented phyla. An increase in Firmicutes (58.3±16 to 61.4±13.3, p = 0.68) and a reduction in Bacteroidetes (32.6±14.8 to 30.3±11.4, p = 0.51) have been registered with the increase of PA level. A higher variability (expressed as Shannon α-index) has been detected in minimally active (3.39±0.03) and HEPA-active (3.41±0) individuals respect to inactive subjects (3.35±0.07) (p = 0.05). Conclusions Even if they are not significant, these preliminary results suggest a relationship between PA levels and gut microbiota composition. An active lifestyle seems to be associated with a greater microbial diversity in the gut. Further researches are needed to explain these findings. Key messages Physical activity seems to be associated with gut microbiota composition. A greater variability in gut microbiota was found in active people.

scholarly journals Longitudinal Investigation of the Gut Microbiota in Goat Kids from Birth to Postweaning

2020 ◽  
Vol 8 (8) ◽  
pp. 1111 ◽  
Author(s):  
Yimin Zhuang ◽  
Jianmin Chai ◽  
Kai Cui ◽  
Yanliang Bi ◽  
Qiyu Diao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Temporal Dynamics ◽  
Later Life ◽  
Shannon Index ◽  
Microbial Colonization ◽  
Feeding Strategies ◽  
Microbial Composition ◽  
Linear Discriminant ◽  
Next Generation Sequencing Technology ◽  
Distinct Structure

Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray–Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1–d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production.

scholarly journals Anti-Acid Drug Treatment Induces Changes in the Gut Microbiome Composition of Hemodialysis Patients

2021 ◽  
Vol 9 (2) ◽  
pp. 286
Author(s):  
Yi-Ting Lin ◽  
Ting-Yun Lin ◽  
Szu-Chun Hung ◽  
Po-Yu Liu ◽  
Ping-Hsun Wu ◽  
...  
Keyword(s):  
Random Forest ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Hemodialysis Patients ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Linear Discriminant ◽  
H2 Blocker ◽  
Α Diversity ◽  
16S Rna

Anti-acid drugs, proton pump inhibitor (PPI) and histamine-2 blocker (H2-blocker), are commonly prescribed to treat gastrointestinal disorders. These anti-acid drugs alter gut microbiota in the general population, but their effects are not known in hemodialysis patients. Hence, we investigated the microbiota composition in hemodialysis patients treated with PPIs or H2-blocker. Among 193 hemodialysis patients, we identified 32 H2-blocker users, 23 PPI users, and 138 no anti-acid drug subjects. Fecal samples were obtained to analyze the gut microbiome using 16S RNA amplicon sequencing. Differences in the microbial composition of the H2-blocker users, PPI users, and controls were assessed using linear discriminant analysis effect size and the random forest algorithm. The species richness or evenness (α-diversity) was similar among the three groups, whereas the inter-individual diversity (β-diversity) was different between H2-blocker users, PPI users, and controls. Hemodialysis patients treated with H2-blocker and PPIs had a higher microbial dysbiosis index than the controls, with a significant increase in the genera Provetella 2, Phascolarctobacterium, Christensenellaceae R-7 group, and Eubacterium oxidoreducens group in H2-blocker users, and Streptococcus and Veillonella in PPI users. In addition, compared to the H2-blocker users, there was a significant enrichment of the genera Streptococcus in PPI users, as confirmed by the random forest analysis and the confounder-adjusted regression model. In conclusion, PPIs significantly changed the gut microbiota composition in hemodialysis patients compared to H2-blocker users or controls. Importantly, the Streptococcus genus was significantly increased in PPI treatment. These findings caution against the overuse of PPIs.

scholarly journals Kefir Peptides Prevent Estrogen Deficiency-Induced Bone Loss and Modulate the Structure of the Gut Microbiota in Ovariectomized Mice

Nutrients ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3432
Author(s):  
Min-Yu Tu ◽  
Kuei-Yang Han ◽  
Gary Ro-Lin Chang ◽  
Guan-Da Lai ◽  
Ku-Yi Chang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Milk Proteins ◽  
Amplicon Sequencing ◽  
Estrogen Deficiency ◽  
Osteoporosis Prevention ◽  
Mineral Density ◽  
Bacterial Populations ◽  
Ovariectomized Mice ◽  
Α Diversity ◽  
16S Rdna Amplicon Sequencing

Osteoporosis is a major skeletal disease associated with estrogen deficiency in postmenopausal women. Kefir-fermented peptides (KPs) are bioactive peptides with health-promoting benefits that are produced from the degradation of dairy milk proteins by the probiotic microflora in kefir grains. This study aimed to evaluate the effects of KPs on osteoporosis prevention and the modulation of the composition of the gut microbiota in ovariectomized (OVX) mice. OVX mice receiving an 8-week oral gavage of 100 mg of KPs and 100 mg of KPs + 10 mg Ca exhibited lower trabecular separation (Tb. Sp), and higher bone mineral density (BMD), trabecular number (Tb. N) and bone volume (BV/TV), than OVX groups receiving Ca alone and untreated mice, and these effects were also reflected in bones with better mechanical properties of strength and fracture toughness. The gut microbiota of the cecal contents was examined by 16S rDNA amplicon sequencing. α-Diversity analysis indicated that the gut microbiota of OVX mice was enriched more than that of sham mice, but the diversity was not changed significantly. Treatment with KPs caused increased microbiota richness and diversity in OVX mice compared with those in sham mice. The microbiota composition changed markedly in OVX mice compared with that in sham mice. Following the oral administration of KPs for 8 weeks, the abundances of Alloprevotella, Anaerostipes, Parasutterella, Romboutsia, Ruminococcus_1 and Streptococcus genera were restored to levels close to those in the sham group. However, the correlation of these bacterial populations with bone metabolism needs further investigation. Taken together, KPs prevent menopausal osteoporosis and mildly modulate the structure of the gut microbiota in OVX mice.

scholarly journals Comparative Analysis of the Gut Microbial Composition and Meat Flavor of Two Chicken Breeds in Different Rearing Patterns

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Jing Sun ◽  
Yan Wang ◽  
Nianzhen Li ◽  
Hang Zhong ◽  
Hengyong Xu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Solid Phase Microextraction ◽  
Solid Phase ◽  
Flavor Compounds ◽  
Microbial Composition ◽  
Ethyl Hexanoate ◽  
Rdna Genes ◽  
Meat Flavor ◽  
Chicken Breeds ◽  
V3 Region

The objective of the study is to compare the effects of free-range (FR) and cage-range (CR) breeding on gut microbiota and flavor compounds of Caoke (C) and Partridge Shank chickens (Q). A total of 120 experimental chickens were assigned to FR group and CR group; each group contain both 30 Caoke chickens and 30 Partridge Shank chickens. At 154 d old, 12 chickens of each group were selected and their cecal contents were extracted and examined for the composition of gut microbiota by illumina sequencing of the V3 region of the 16S rDNA genes, and flavor compounds were analyzed through headspace-solid-phase microextraction (HS-SPME) method. The results showed that, except for acids, the amount of flavor substances in the FR group was higher than those in the CR group, especially the content of Hexanal and D-limonene. Meanwhile, the higher concentrations of carbonyls including (E,E)-2,4-decadienal, (E)-2-decenal, (E)-2-octenal, and pentanal were in the FR chicken meat, but the differences in concentrations compared with CR were not significant. High levels of ethyl hexanoate and β-ocimene were only detected in FR groups. The Firmicutes had the highest proportion of chicken cecal microbiota, whereas the Fusobacteria was only detected in the cecal samples of Q chicken in FR group. Actinobacteria was more prevalent in FR groups than in CR groups. Meanwhile, in Q chickens, the proportions of Bacteroidetes and Proteobacteria in FR group were higher than those in CR group. Using MG-RAST Subsystem Technology, we found that some genes were associated with the formation of precursors of flavor compounds or with the metabolism and degradation of aromatic compounds. Overall, CR and FR breeding influenced the gut microbiota and flavor compounds, potentially because of the changes in diet and living conditions.

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