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 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 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 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 The Effect of Lactobacillus plantarum BW2013 on The Gut Microbiota in Mice Analyzed by 16S rRNA Amplicon Sequencing

2021 ◽  
Vol 70 (2) ◽  
pp. 235-243
Author(s):  
TONG TONG ◽  
XIAOHUI NIU ◽  
QIAN LI ◽  
YUXI LING ◽  
ZUMING LI ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Dose Group ◽  
Low Dose ◽  
Amplicon Sequencing ◽  
Control Group ◽  
High Dose ◽  
Treatment Groups ◽  
16S Rrna Amplicon Sequencing ◽  
Medium Dose

Lactobacillus plantarum BW2013 was isolated from the fermented Chinese cabbage. This study aimed to test the effect of this strain on the gut microbiota in BALB/c mice by 16S rRNA amplicon sequencing. The mice were randomly allocated to the control group and three treatment groups of L. plantarum BW2013 (a low-dose group of 108 CFU/ml, a medium-dose group of 109 CFU/ml, and a high-dose group of 1010 CFU/ml). The weight of mice was recorded once a week, and the fecal samples were collected for 16S rRNA amplicon sequencing after 28 days of continuous treatment. Compared with the control group, the body weight gain in the treatment groups was not significant. The 16S rRNA amplicon sequencing analysis showed that both the Chao1 and ACE indexes increased slightly in the medium-dose group compared to the control group, but the difference was not significant. Based on PCoA results, there was no significant difference in β diversity between the treatment groups. Compared to the control group, the abundance of Bacteroidetes increased in the low-dose group. The abundance of Firmicutes increased in the medium-dose group. At the genus level, the abundance of Alloprevotella increased in the low-dose group compared to the control group. The increased abundance of Ruminococcaceae and decreased abundance of Candidatus_Saccharimonas was observed in the medium-dose group. Additionally, the abundance of Bacteroides increased, and Alistipes and Candidatus_Saccharimonas decreased in the high-dose group. These results indicated that L. plantarum BW2013 could ameliorate gut microbiota composition, but its effects vary with the dose.

scholarly journals Quantitative insights into effects of intrapartum antibiotics and birth mode on infant gut microbiota in relation to well-being during the first year of life

2021 ◽  
Author(s):  
Katri Korpela ◽  
Roosa Jokela ◽  
Ching Jian ◽  
Evgenia Dikareva ◽  
Anne Nikkonen ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Community Dynamics ◽  
Gastrointestinal Symptoms ◽  
Well Being ◽  
Amplicon Sequencing ◽  
First Year ◽  
Rrna Gene ◽  
Absolute Abundance ◽  
Abundance Estimates ◽  
First Year Of Life

Background and aims Caesarean section (CS)-birth and maternally administered intrapartum antibiotics (IP) affect colonization of the neonate. We compared the effects of CS delivery and IP antibiotics on infant gut microbiota development and wellbeing over the first year. To understand the developing community dynamics, we focused on absolute bacterial abundance estimates over relative abundances. Methods We studied 144 healthy infants born between gestational weeks 37-42 vaginally without antibiotics (N=58), with IP penicillin (N=25) or cephalosporin (N=13), or by CS with IP cephalosporin (N=34) or other antibiotics (N=14). Gut microbiota composition and temporal development was analysed at 5-7 time points during the first year of life using 16S rRNA gene amplicon sequencing, complemented with qPCR to obtain absolute abundance estimates in 92 infants. A mediation analysis was carried out to identify taxa linked to gastrointestinal function and discomfort (crying, defecation frequency and signs of gastrointestinal symptoms) and birth interventions. Results Based on absolute abundance estimates, depletion of Bacteroides spp. was specific to CS birth while decreased bifidobacteria and increased Bacilli were common to CS birth and exposure to IP antibiotics in vaginal delivery. Abundance of numerous taxa differed between the birth modes among cephalosporin-exposed infants. Penicillin had a milder impact on the infant gut microbiota than cephalosporin. The effects of both CS birth and IP antibiotics on infant gut microbiota associated with increased gastrointestinal symptoms during the first months. Conclusion CS birth and maternal IP antibiotics have both specific and overlapping effects on infant gut microbiota development. The resulting microbiota deviations were found to associate with gastrointestinal symptoms in infancy.

scholarly journals SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

2021 ◽  
Author(s):  
Giulia Agostinetto ◽  
Davide Bozzi ◽  
Danilo Porro ◽  
Maurizio Casiraghi ◽  
Massimo Labra ◽  
...  
Keyword(s):  
Data Science ◽  
Data Retrieval ◽  
Amplicon Sequencing ◽  
Full Potential ◽  
Skin Microbiome ◽  
Data Accessibility ◽  
16S Rrna Amplicon Sequencing ◽  
Comprehensive Collection ◽  
Microbiome Research ◽  
Microbiome Data

Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amount of data lacks harmonization and is far from being completely exploited in its full potential to build a foundation that places microbiome research at the nexus of many subdisciplines within and beyond biology. Thus, urges the need for data accessibility and reusability, according to FAIR (Findable, Accessible, Interoperable, and Reusable) principles, as supported by National Microbiome Data Collaborative and FAIR Microbiome. To tackle the challenge of accelerating discovery and advances in skin microbiome research, we collected, integrated and organized existing microbiome data resources from human skin 16S rRNA amplicon sequencing experiments. We generated a comprehensive collection of datasets, enriched in metadata, and organized this information into data frames ready to be integrated into microbiome research projects and advanced post-processing analysis, such as data science applications (e.g. machine learning). Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them. Lastly, we highlighted some caveats regarding metadata retrieval and suggested ways to improve future metadata submissions. Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field.

scholarly journals Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate

2021 ◽  
Author(s):  
Alice Baniel ◽  
Lauren Petrullo ◽  
Arianne Mercer ◽  
Laurie Reitsema ◽  
Sierra Sams ◽  
...  
Keyword(s):  
Maternal Effects ◽  
Gut Microbiome ◽  
Early Life ◽  
Amplicon Sequencing ◽  
Microbial Colonization ◽  
Fecal Samples ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Gut Colonization ◽  
First Time

Early-life gut microbial colonization is an important process shaping host physiology, immunity and long-term health outcomes in humans and other animals. However, our understanding of this dynamic process remains poorly investigated in wild animals, where developmental mechanisms can be better understood within ecological and evolutionary relevant contexts. Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas (Theropithecus gelada), we characterized gut microbiome maturation during the first three years of life and assessed the role of maternal effects in shaping offspring microbiome assembly. Microbial diversity increased rapidly in the first months of life, followed by more gradual changes until weaning. As expected, changes in gut microbiome composition and function with increasing age reflected progressive dietary transitions: in early infancy when infants rely heavily on their mother's milk, microbes that facilitate milk glycans and lactose utilization dominated, while later in development as graminoids are progressively introduced into the diet, microbes that metabolize plant complex polysaccharides became dominant. Furthermore, the microbial community of nursing infants born to first-time (primiparous) mothers was more "milk-oriented" compared to similarly-aged infants born to experienced (multiparous) mothers. Comparisons of matched mother-offspring fecal samples to random dyads did not support vertical transmission as a conduit for these maternal effects, which instead could be explained by slower phenotypic development (and associated slower gut microbiome maturation) in infants born to first-time mothers. Together, our findings highlight the dynamic nature of gut colonization

scholarly journals Korean Traditional Medicine (Jakyakgamcho-tang) Ameliorates Colitis by Regulating Gut Microbiota

Metabolites ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 226 ◽  
Author(s):  
Seung-Ho Seo ◽  
Tatsuya Unno ◽  
Seong-Eun Park ◽  
Eun-Ju Kim ◽  
Yu-Mi Lee ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Control Group ◽  
Scaling Analysis ◽  
Aminosalicylic Acid ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Cytokine Levels ◽  
Korean Traditional Medicine ◽  
Gut Microbial Community

The objective of this study was to examine the anti-colitis activity of Jakyakgamcho-tang (JGT) in dextran sulfate sodium (DSS)-induced colitis and explore changes of the gut microbial community using 16S rRNA amplicon sequencing and metabolomics approaches. It was found that treatment with JGT or 5-aminosalicylic acid (5-ASA) alleviated the severity of colitis symptoms by suppressing inflammatory cytokine levels of IL-6, IL-12, and IFN-γ. The non-metric multidimensional scaling analysis of gut microbiome revealed that JGT groups were clearly separated from the DSS group, suggesting that JGT administration altered gut microbiota. The operational taxonomic units (OTUs) that were decreased by DSS but increased by JGT include Akkermansia and Allobaculum. On the other hand, OTUs that were increased by DSS but decreased by 5-ASA or JGT treatments include Bacteroidales S24-7, Ruminococcaceae, and Rikenellaceae, and the genera Bacteroides, Parabacteroides, Oscillospira, and Coprobacillus. After JGT administration, the metabolites, including most amino acids and lactic acid that were altered by colitis induction, became similar to those of the control group. This study demonstrates that JGT might have potential to effectively treat colitis by restoring dysbiosis of gut microbiota and host metabolites.

scholarly journals Gut Microbiota Modulation by Dietary Barley Malt Melanoidins

Nutrients ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 241 ◽  
Author(s):  
Nesreen Aljahdali ◽  
Pascale Gadonna-Widehem ◽  
Pauline M. Anton ◽  
Franck Carbonero
Keyword(s):  
Fatty Acids ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Short Chain Fatty Acids ◽  
Control Group ◽  
Maillard Reaction Products ◽  
Reaction Products ◽  
Barley Malt ◽  
16S Rrna Amplicon Sequencing ◽  
The Impact

Melanoidins are the final Maillard reaction products (protein–carbohydrate complexes) produced in food by prolonged and intense heating. We assessed the impact of the consumption of melanoidins from barley malts on gut microbiota. Seventy-five mice were assigned into five groups, where the control group consumed a non-melanoidin malt diet, and other groups received melanoidin-rich malts in increments of 25% up to 100% melanoidin malts. Feces were sampled at days 0, 1, 2, 3, 7, 14, and 21 and the microbiota was determined using V4 bacterial 16S rRNA amplicon sequencing and short-chain fatty acids (SCFA) by gas chromatography. Increased melanoidins was found to result in significantly divergent gut microbiota profiles and supported sustained SCFA production. The relative abundance of Dorea, Oscillibacter, and Alisitpes were decreased, while Lactobacillus, Parasutterella, Akkermansia, Bifidobacterium, and Barnesiella increased. Bifidobacterium spp. and Akkermansia spp. were significantly increased in mice consuming the highest melanoidin amounts, suggesting remarkable prebiotic potential.

scholarly journals Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shoichiro Kameoka ◽  
Daisuke Motooka ◽  
Satoshi Watanabe ◽  
Ryuichi Kubo ◽  
Nicolas Jung ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Analysis Data ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Sequencing Technologies ◽  
Primer Sets ◽  
Microbiome Data

Abstract Background 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1–V2 (V12) and the standard V3–V4 primer (V34) sets to optimize the gut microbiota analysis protocol. Results QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data. Conclusions These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.

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