scholarly journals Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota

2018 ◽  
Author(s):  
Wei Yan ◽  
Jiangxia Zheng ◽  
Chaoliang Wen ◽  
Congliang Ji ◽  
Dexiang Zhang ◽  
...  
Keyword(s):  
Small Intestine ◽  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Fecal Samples ◽  
Community Membership ◽  
16S Rrna Amplicon Sequencing ◽  
Fecal Sampling

AbstractBackgroundDespite the convenience and noninvasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum and feces samples, for 16S rRNA amplicon sequencing analyses.ResultsIn this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11 – 87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54 – 0.71 and 0.71 – 0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the 4 gut segments, and these correlations were not high (ρ = −0.2 – 0.4, P < 0.05) for most genera.ConclusionsOur results provide evidence that the good potential of feces to identify most taxa in chicken guts, but it should be interpreted with caution by using feces as a proxy for gut in microbial structure analyses. This work provides insights and future directions regarding the usage of fecal samples in studies of the gut microbiome.

scholarly journals Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1938
Author(s):  
Han Aricha ◽  
Huasai Simujide ◽  
Chunjie Wang ◽  
Jian Zhang ◽  
Wenting Lv ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Inner Mongolia ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Composition Analysis ◽  
Geographical Factors ◽  
Rrna Sequencing ◽  
Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

scholarly journals Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study

2021 ◽  
Vol 9 (6) ◽  
pp. 1237
Author(s):  
Han-Na Kim ◽  
Eun-Jeong Joo ◽  
Chil-Woo Lee ◽  
Kwang-Sung Ahn ◽  
Hyung-Lae Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gastrointestinal Symptoms ◽  
Amplicon Sequencing ◽  
Recovery Phase ◽  
Fecal Samples ◽  
Intestinal Microbes ◽  
Gut Dysbiosis ◽  
16S Rrna Amplicon Sequencing ◽  
Microbiome Data ◽  
Negative Conversion

Patients with COVID-19 have been reported to experience gastrointestinal symptoms as well as respiratory symptoms, but the effects of COVID-19 on the gut microbiota are poorly understood. We explored gut microbiome profiles associated with the respiratory infection of SARS-CoV-2 during the recovery phase in patients with asymptomatic or mild COVID-19. A longitudinal analysis was performed using the same patients to determine whether the gut microbiota changed after recovery from COVID-19. We applied 16S rRNA amplicon sequencing to analyze two paired fecal samples from 12 patients with asymptomatic or mild COVID-19. Fecal samples were selected at two time points: during SARS-CoV-2 infection (infected state) and after negative conversion of the viral RNA (recovered state). We also compared the microbiome data with those from 36 healthy controls. Microbial evenness of the recovered state was significantly increased compared with the infected state. SARS-CoV-2 infection induced the depletion of Bacteroidetes, while an abundance was observed with a tendency to rapidly reverse in the recovered state. The Firmicutes/Bacteroidetes ratio in the infected state was markedly higher than that in the recovered state. Gut dysbiosis was observed after infection even in patients with asymptomatic or mild COVID-19, while the composition of the gut microbiota was recovered after negative conversion of SARS-CoV-2 RNA. Modifying intestinal microbes in response to COVID-19 might be a useful therapeutic alternative.

scholarly journals H. pylori Eradication Treatment Alters Gut Microbiota and GLP-1 Secretion in Humans

2019 ◽  
Vol 8 (4) ◽  
pp. 451 ◽  
Author(s):  
Isabel Cornejo-Pareja ◽  
Gracia Martín-Núñez ◽  
M. Roca-Rodríguez ◽  
Fernando Cardona ◽  
Leticia Coin-Aragüez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Carbohydrate Metabolism ◽  
Eradication Therapy ◽  
Amplicon Sequencing ◽  
Antibiotic Use ◽  
Metabolic Disturbances ◽  
Bifidobacterium Adolescentis ◽  
16S Rrna Amplicon Sequencing ◽  
H Pylori

Changes in the intestinal microbial community and some metabolic disturbances, including obesity and type2 diabetes, are related. Glucagon-like peptide-1 (GLP-1) regulates glucose homeostasis. Microbiota have been linked to incretin secretion. Antibiotic use causes changes in microbial diversity and composition. Our aim was to evaluate the relationship between microbiota changes and GLP-1 secretion. A prospective case-control study with a Helicobacter pylori-positive patient model involving subjects under eradication therapy (omeprazole, clarithromycin, and amoxicillin). Forty patients with H. pylori infection and 20 matched participants, but negative for H. pylori antigen. Patients were evaluated before and two months after treatment. We analyzed anthropometric measurements, carbohydrate metabolism, lipid profile, and C-reactive protein. Gut microbiota composition was analyzed through 16S rRNA amplicon sequencing (IlluminaMiSeq). Eradication treatment for H. pylori decreased bacterial richness (Chao1, p = 0.041). Changes in gut microbiota profiles were observed at phylum, family, genus and species levels. GLP-1 secretion and variables of carbohydrate metabolism were improved. Correlations were seen between GLP-1 changes and variations within microbial community abundances, specifically Bifidobacterium adolescentis, the Lachnobacterium genus, and Coriobacteriaceae family. A conventional treatment to eradicate H. pylori could improve carbohydrate metabolism possibly in relation with an increase in GLP-1 secretion. GLP-1 secretion may be related to alterations in intestinal microbiota, specifically Lachnobacterium, B. adolescentis and Coriobacteriaceae.

scholarly journals Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1718
Author(s):  
Kelang Kang ◽  
Yan Hu ◽  
Shu Wu ◽  
Shourong Shi
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Fecal Microbiota ◽  
Metagenomic Analysis ◽  
Fecal Samples ◽  
Microbial Community Function ◽  
Community Function ◽  
Rectal Swabs ◽  
Gut Microbial Community

When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

scholarly journals On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples

2021 ◽  
Author(s):  
Shan Sun ◽  
Xiangzhu Zhu ◽  
Xiang Huang ◽  
Harvey J. Murff ◽  
Reid M. Ness ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Mucosal Tissue ◽  
Tissue Samples ◽  
16S Rrna Amplicon Sequencing ◽  
Functional Profiles

AbstractThe gut microbiota plays an important role in human health and disease. Stool, swab and mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. We previously reported differences in microbial community composition with 16S rRNA amplicon sequencing between stool, swab and mucosal tissue samples. Here, we extended the previous study to a larger cohort and performed shotgun metagenome sequencing of 1,397 stool, swab and mucosal tissue samples from 240 participants. Consistent with previous results, taxonomic composition of stool and swab samples was distinct, but still more similar to each other than mucosal tissue samples, which had a substantially different community composition, characterized by a high relative abundance of the mucus metabolizers Bacteroides and Subdoligranulum, as well as bacteria with higher tolerance for oxidative stress such as Escherichia. As has been previously reported, functional profiles were more uniform across sample types than taxonomic profiles with differences between stool and swab samples smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles of different sample types were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or swab gave broadly similar results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for the experimental design of studies aimed to understand microbiota perturbations specific to defined micro niches within the human intestinal tract.

scholarly journals Relationships between Gut Microbiota, Metabolome, Body Weight, and Glucose Homeostasis of Obese Dogs Fed with Diets Differing in Prebiotic and Protein Content

2020 ◽  
Vol 8 (4) ◽  
pp. 513 ◽  
Author(s):  
Emmanuelle Apper ◽  
Lisa Privet ◽  
Bernard Taminiau ◽  
Cindy Le Bourgot ◽  
Ljubica Svilar ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Glucose Homeostasis ◽  
Energy Homeostasis ◽  
Latin Square ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Protein Levels ◽  
16S Rrna Amplicon Sequencing ◽  
Metabolic Dysfunctions ◽  
Nutritional Strategies

Obesity is a major issue in pets and nutritional strategies need to be developed, like promoting greater protein and fiber intake. This study aimed to evaluate the effects of dietary protein levels and prebiotic supplementation on the glucose metabolism and relationships between the gut, microbiota, metabolome, and phenotype of obese dogs. Six obese Beagle dogs received a diet containing 25.6% or 36.9% crude protein, with or without 1% short-chain fructo-oligosaccharide (scFOS) or oligofructose (OF), in a Latin-square study design. Fecal and blood samples were collected for metabolite analysis, untargeted metabolomics, and 16S rRNA amplicon sequencing. A multi-block analysis was performed to build a correlation network to identify relationships between fecal microbiota, metabolome, and phenotypic variables. Diets did not affect energy homeostasis, but scFOS supplementation modulated fecal microbiota composition and induced significant changes of the fecal metabolome. Bile acids and several amino acids were related to glucose homeostasis while specific bacteria gathered in metavariables had a high number of links with phenotypic and metabolomic parameters. It also suggested that fecal aminoadipate and hippurate act as potential markers of glucose homeostasis. This preliminary study provides new insights into the relationships between the gut microbiota, the metabolome, and several phenotypic markers involved in obesity and associated metabolic dysfunctions.

scholarly journals Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 999
Author(s):  
Helena Torrell ◽  
Adrià Cereto-Massagué ◽  
Polina Kazakova ◽  
Lorena García ◽  
Héctor Palacios ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Variable Region ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Intestinal Microbiome ◽  
Fecal Samples ◽  
16S Rrna Amplicon Sequencing ◽  
Method Optimization ◽  
Feature Selection Approach

Background: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples. Methods: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis. Results: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile. Conclusion: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.

scholarly journals The Maternal Milk Microbiome in Mammals of Different Types and Its Potential Role in the Neonatal Gut Microbiota Composition

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3349
Author(s):  
Yile Ge ◽  
Wei Zhu ◽  
Lu Chen ◽  
Diyan Li ◽  
Qingqing Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Excision Repair ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Nucleotide Metabolism ◽  
Source Tracking ◽  
Maternal Milk ◽  
16S Rrna Amplicon Sequencing ◽  
Host Diet ◽  
Base Excision

Maternal milk, a main source of nutrition for neonates in early life, has attracted attention. An increasing number of studies have found that maternal milk has a high microbial diversity, as well as factors that might influence this diversity. However, there is a lack of knowledge regarding the effects of host diet and phylogeny on maternal milk microbes and the contribution of the maternal milk microbiota to the neonatal gut microbiota. Here, we analyzed the maternal milk and fecal microbiota of nine species (lion, dog, panda, human, mouse, rhesus macaque, cow, goat, and rabbit) of mammals of three type groups (herbivore, omnivore, and carnivore) using 16S rRNA amplicon sequencing. Our study provided evidence of host diet and phylogeny on the maternal milk microbiota. Moreover, functional prediction revealed that the carnivores had a significantly higher percentage of base excision repair, glycerolipid metabolism, taurine and hypotaurine metabolism, inorganic ion transport and metabolism, and nucleotide metabolism; while arginine and proline metabolism showed enrichment in the herbivore group. Source-tracking analysis showed that the contributions of bacteria from maternal milk to the microbiota of neonates of different mammals were different at day 3 after neonatal birth. Overall, our findings provided a theoretical basis for the maternal milk microbiota to affect neonatal fecal microbiota at day 3 after neonatal birth.

scholarly journals Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota

2021 ◽  
Author(s):  
A. Checcucci ◽  
D. Luise ◽  
M. Modesto ◽  
F. Correa ◽  
P. Bosi ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Metabolic Activity ◽  
Fecal Sample ◽  
Storage Conditions ◽  
Fecal Microbiota ◽  
Host Animal ◽  
Metabolic Potential ◽  
Fecal Samples ◽  
Feces Sample

Abstract In the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the BiologTM Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at −80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at −80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. BiologTM Ecoplates technology is a rapid and useful method to explore microbial communities’ metabolism in animal fecal samples contributing to investigate host animal physiology. Key points • Freezing of samples can preserve the functional activity of the aerotolerant microbial community for 150 days. • The concentration of microbial cells strongly influences metabolic activity detection. • Sequencing coupled with the BiologTMEcoplates could be a strategy to evaluate the metabolic potential of the microbiota of the fecal sample. Graphical abstract

scholarly journals 16S rRNA Amplicon Sequencing of Seawater Microbiota from Quintero Bay, Chile, Affected by Oil Spills, Shows the Presence of an Oil-Degrading Marine Bacterial Guild Structured by the Bacterial Genera Alcanivorax, Cobetia, Halomonas, and Oleiphilus

2018 ◽  
Vol 7 (21) ◽  
Author(s):  
Claudia Ibacache-Quiroga ◽  
Juan Ojeda ◽  
M. Alejandro Dinamarca
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Microbial Community Structure ◽  
Oil Spills ◽  
Amplicon Sequencing ◽  
Central Coast ◽  
The Past ◽  
16S Rrna Amplicon Sequencing ◽  
Seawater Samples

The Quintero Bay, located along the central coast of Chile, has suffered different oil spills during the past 5 years, impacting marine ecosystems. This report describes the microbial community structure of seawater samples obtained from the Quintero Bay through 16S rRNA amplicon sequencing.

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