Cross-Sectional Analysis of the Microbiota of Human Gut and Its Direct Environment in a Household Cohort with High Background of Antibiotic Use

Comprehensive insight into the microbiota of the gut of humans and animals, as well as their living environment, in communities with a high background of antibiotic use and antibiotic resistance genes is scarce. Here, we used 16S rRNA gene sequencing to describe the (dis)similarities in the microbiota of feces from humans (n = 107), domestic animals (n = 36), water (n = 89), and processed food (n = 74) in a cohort with individual history of antibiotic use in northern Vietnam. A significantly lower microbial diversity was observed among individuals who used antibiotics in the past 4 months (n = 44) compared to those who did not (n = 63). Fecal microbiota of humans was more diverse than nonhuman samples and shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4% (3.2–9.9)), water (2.2% (1.2–2.8)), and food (3.1% (1.5–3.1)). Sharing of ASVs between humans and companion animals was not associated with the household. However, we did observe a correlation between an Enterobacteriaceae ASV and the presence of extended-spectrum beta-lactamase CTX-M-group-2 encoding genes in feces from humans and animals (p = 1.6 × 10−3 and p = 2.6 × 10−2, respectively), hinting toward an exchange of antimicrobial-resistant strains between reservoirs.

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Cross-sectional analysis of the microbiota of human gut and their direct environment (exposome) in a household cohort in northern Vietnam

10.1101/2021.02.23.432416 ◽

2021 ◽

Author(s):

Vu Thi Ngoc Bich ◽

Ho Bich Hai ◽

Gianluca Galazzo ◽

Vu Tien Viet Dung ◽

Melissa Oomen ◽

...

Keyword(s):

Companion Animals ◽

Antibiotic Resistance Genes ◽

Antibiotic Use ◽

Fecal Microbiota ◽

Human Gut ◽

Cross Sectional ◽

High Background ◽

Geographical Cluster ◽

Resistant Strains ◽

Sectional Analysis

AbstractComprehensive insight into the human gut microbiota and the interaction with their environment in communities with a high background of antibiotic use and antibiotic resistance genes is currently largely lacking. In a cohort (Vietnam), individuals within the same household, also individuals within their geographical cluster share more bacterial taxa than individuals from different households or geographical clusters. The microbial diversity among individuals who used antibiotics in the past four months was significantly lower than those who did not. Fecal microbiota of humans was more diverse than non-human samples, shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4%), water (2.2%) and food (3.1%). Sharing of ASVs between humans and companion animals was not associated with household. There is a correlation between an Enterobacteriaceae ASV and the presence of blactx-m-2 in feces from humans and animals, hinting towards an exchange of antimicrobial resistant strains between reservoirs.

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Characterization of C. difficile strains isolated from companion animals and the associated changes in the host fecal microbiota

10.1101/822577 ◽

2019 ◽

Cited By ~ 3

Author(s):

R. Thanissery ◽

M.R. McLaren ◽

A. Rivera ◽

Amber D. Reed ◽

N.S. Betrapally ◽

...

Keyword(s):

Gut Microbiota ◽

Companion Animals ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Gene Profiling ◽

Human Populations ◽

Toxin Gene ◽

Rrna Gene ◽

Colonization Resistance

AbstractBackgroundClostridioides difficile is an enteric pathogen historically known to cause hospital associated (HA)-infections in humans. A major risk factor for CDI in humans is antibiotic usage as it alters the gut microbiota and there is a loss of colonization resistance against C. difficile. In recent years there has been an increase in community associated (CA)-C. difficile infection that does not have the same risk factors as HA-CDI. Potential sources of CA-CDI have been proposed and include animals, food, water, and the environment, however these sources remain poorly investigated. Here, we define the prevalence of C. difficile strains found in different companion animals (canines, felines, and equines) to investigate a potential zoonotic link. C. difficile strains were identified by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16s rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts.ResultsHere, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes, with overlap between HA- and CA-CDI cases in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridia C. hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.ConclusionsIn this study we investigated a potentially important source of C. difficile transmission: the companion animal population. C. difficile carriage was common in dogs, cats, and horses. C. difficile isolates from companion animals included many of the same ribotypes known to cause HA- and CA-CDI in humans, and had similar antimicrobial resistance profiles as those isolated from human populations. These data contribute to our understanding of non-hospital exposure to C. difficile in the human population and suggest new avenues for reducing C. difficile prevalence in companion animals and, perhaps, thereby reducing CA-CDI in humans.

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Links between fecal microbiota and the response to vaccination against influenza A virus in pigs

npj Vaccines ◽

10.1038/s41541-021-00351-2 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Marion Borey ◽

Fany Blanc ◽

Gaëtan Lemonnier ◽

Jean-Jacques Leplat ◽

Deborah Jardet ◽

...

Keyword(s):

Immune Response ◽

Influenza A Virus ◽

Influenza A ◽

16S Rrna Gene Sequencing ◽

Serum Levels ◽

Fecal Microbiota ◽

Rrna Gene ◽

Vaccine Response ◽

Specific Igg ◽

Rrna Gene Sequencing

AbstractThis study describes the associations between fecal microbiota and vaccine response variability in pigs, using 98 piglets vaccinated against the influenza A virus at 28 days of age (D28) with a booster at D49. Immune response to the vaccine is measured at D49, D56, D63, and D146 by serum levels of IAV-specific IgG and assays of hemagglutination inhibition (HAI). Analysis of the pre-vaccination microbiota characterized by 16S rRNA gene sequencing of fecal DNA reveals a higher vaccine response in piglets with a richer microbiota, and shows that 23 operational taxonomic units (OTUs) are differentially abundant between high and low IAV-specific IgG producers at D63. A stronger immune response is linked with OTUs assigned to the genus Prevotella and family Muribaculaceae, and a weaker response is linked with OTUs assigned to the genera Helicobacter and Escherichia-Shigella. A set of 81 OTUs accurately predicts IAV-specific IgG and HAI titer levels at all time points, highlighting early and late associations between pre-vaccination fecal microbiota composition and immune response to the vaccine.

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Abrupt Temporal Fluctuations in the Chicken Fecal Microbiota Are Explained by Its Gastrointestinal Origin

Applied and Environmental Microbiology ◽

10.1128/aem.05391-11 ◽

2012 ◽

Vol 78 (8) ◽

pp. 2941-2948 ◽

Cited By ~ 65

Author(s):

M. Sekelja ◽

I. Rud ◽

S. H. Knutsen ◽

V. Denstadli ◽

B. Westereng ◽

...

Keyword(s):

Barrier Function ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Pathogen Transmission ◽

Rrna Gene ◽

Multivariate Statistical ◽

Content Type ◽

Factors Affecting ◽

Temporal Fluctuations ◽

Gastric Barrier

ABSTRACTOne of the main challenges in understanding the composition of fecal microbiota is that it can consist of microbial mixtures originating from different gastrointestinal (GI) segments. Here, we addressed this challenge for broiler chicken feces using a direct 16S rRNA gene-sequencing approach combined with multivariate statistical analyses. Broiler feces were chosen because of easy sampling and the importance for pathogen transmission to the human food chain. Feces were sampled daily for 16 days from chickens with and without a feed structure-induced stimulation of the gastric barrier function. Overall, we found four dominant microbial phylogroups in the feces. Two of the phylogroups were related to clostridia, one to lactobacilli, and one toEscherichia/Shigella. The relative composition of these phylogroups showed apparent stochastic temporal fluctuations in feces. Analyses of dissected chickens at the end of the experiment, however, showed that the two clostridial phylogroups were correlated to the microbiota in the cecum/colon and the small intestine, while the upper gut (crop and gizzard) microbiota was correlated to the lactobacillus phylogroup. In addition, chickens with a stimulated gizzard also showed less of the proximate GI dominating bacterial group in the feces, supporting the importance of the gastric barrier function. In conclusion, our results suggest that GI origin is a main determinant for the chicken fecal microbiota composition. This knowledge will be important for future understanding of factors affecting shedding of both harmful and beneficial gastrointestinal bacteria through feces.

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

Journal of Translational Medicine ◽

10.1186/s12967-021-03040-9 ◽

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.

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Characterization of bacteria and antibiotic resistance in commercially-produced cheeses sold in China

Journal of Food Protection ◽

10.4315/jfp-21-198 ◽

2021 ◽

Author(s):

Jinghui Yao ◽

Jing Gao ◽

Jianming Guo ◽

Hengan Wang ◽

En Zhang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Lactic Acid ◽

Lactic Acid Bacteria ◽

Acquired Resistance ◽

Antibiotic Resistance Genes ◽

16S Rrna Gene Sequencing ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Rrna Gene ◽

Rrna Gene Sequencing

The consumption of cheese in China is increasing rapidly. Little is known about the microbiota, the presence of antibiotic-resistant bacteria, or the distribution of antibiotic resistance genes (ARGs) in commercially-produced cheeses sold in China. These are important criteria for evaluating quality and safety. Thus, this study assessed the metagenomics of fifteen types of cheese using 16S rRNA gene sequencing. Fourteen bacterial genera were detected. Lactococcus , Lactobacillus , and Streptococcus were dominant based on numbers of sequence reads. Multidrug-resistant lactic acid bacteria were isolated from most of the types of cheese. The isolates showed 100% and 91.7% resistance to streptomycin and sulfamethoxazole, respectively, and genes involved in acquired resistance to streptomycin ( strB) and sulfonamides ( sul2) were detected with high frequency. To analyze the distribution of ARGs in the cheeses in overall, 309 ARGs from eight categories of ARG and nine transposase genes were profiled. A total of 169 ARGs were detected in the 15 cheeses; their occurrence and abundance varied significantly between cheeses. Our study demonstrates that there is various diversity of the bacteria and ARGs in cheeses sold in China. The risks associated with multidrug resistance of dominant lactic acid bacteria are of great concern.

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Oral health and plaque microbial profile in juvenile idiopathic arthritis

Pediatric Rheumatology ◽

10.1186/s12969-019-0387-5 ◽

2019 ◽

Vol 17 (1) ◽

Cited By ~ 2

Author(s):

Sriharsha Grevich ◽

Peggy Lee ◽

Brian Leroux ◽

Sarah Ringold ◽

Richard Darveau ◽

...

Keyword(s):

Juvenile Idiopathic Arthritis ◽

Oral Health ◽

Dental Hygiene ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Microbiota ◽

Gingival Inflammation ◽

Cross Sectional ◽

Dental Patients ◽

Microbial Profile

Abstract Background The oral microbiota has been implicated in the pathogenesis of rheumatoid arthritis through activation of mucosal immunity. This study tested for associations between oral health, microbial communities and juvenile idiopathic arthritis (JIA). Methods A cross-sectional exploratory study of subjects aged 10–18 years with oligoarticular, extended oligoarticular and polyarticular JIA was conducted. Control groups included pediatric dental clinic patients and healthy volunteers. The primary aim was to test for an association between dental health indices and JIA; the secondary aim was to characterize the microbial profile of supragingival plaque using 16S rRNA gene sequencing. Results The study included 85 patients with JIA, 62 dental patients and 11 healthy child controls. JIA patients overall had significantly more gingival inflammation compared to dental patients, as evidenced by bleeding on probing of the gingiva, the most specific sign of active inflammation (p = 0.02). Overall, however, there was a trend towards better dental hygiene in the JIA patients compared to dental patients, based on indices for plaque, decay, and periodontitis. In the JIA patients, plaque microbiota analysis revealed bacteria belonging to genera Haemophilus or Kingella elevated, and Corynebacterium underrepresented. In poly JIA, bacteria belonging to the genus Porphyromonas was overrepresented and Prevotella was underrepresented. Conclusion Increased gingival inflammation in JIA was independent of general oral health, and thus cannot be attributed to poor dental hygiene secondary to disability. The variation of microbial profile in JIA patients could indicate a possible link between gingivitis and synovial inflammation.

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Nuciferine modulates the gut microbiota and prevents obesity in high-fat diet-fed rats

Experimental & Molecular Medicine ◽

10.1038/s12276-020-00534-2 ◽

2020 ◽

Vol 52 (12) ◽

pp. 1959-1975

Author(s):

Yu Wang ◽

Weifan Yao ◽

Bo Li ◽

Shiyun Qian ◽

Binbin Wei ◽

...

Keyword(s):

Lipid Metabolism ◽

Gut Microbiota ◽

Relative Abundance ◽

Metabolic Diseases ◽

Intestinal Barrier ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Low Grade ◽

Rrna Gene Sequencing

AbstractGut microbiota dysbiosis has a significant role in the pathogenesis of metabolic diseases, including obesity. Nuciferine (NUC) is a main bioactive component in the lotus leaf that has been used as food in China since ancient times. Here, we examined whether the anti-obesity effects of NUC are related to modulations in the gut microbiota. Using an obese rat model fed a HFD for 8 weeks, we show that NUC supplementation of HFD rats prevents weight gain, reduces fat accumulation, and ameliorates lipid metabolic disorders. Furthermore, 16S rRNA gene sequencing of the fecal microbiota suggested that NUC changed the diversity and composition of the gut microbiota in HFD-fed rats. In particular, NUC decreased the ratio of the phyla Firmicutes/Bacteroidetes, the relative abundance of the LPS-producing genus Desulfovibrio and bacteria involved in lipid metabolism, whereas it increased the relative abundance of SCFA-producing bacteria in HFD-fed rats. Predicted functional analysis of microbial communities showed that NUC modified genes involved in LPS biosynthesis and lipid metabolism. In addition, serum metabolomics analysis revealed that NUC effectively improved HFD-induced disorders of endogenous metabolism, especially lipid metabolism. Notably, NUC promoted SCFA production and enhanced intestinal integrity, leading to lower blood endotoxemia to reduce inflammation in HFD-fed rats. Together, the anti-obesity effects of NUC may be related to modulations in the composition and potential function of gut microbiota, improvement in intestinal barrier integrity and prevention of chronic low-grade inflammation. This research may provide support for the application of NUC in the prevention and treatment of obesity.

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Alterations of gut microbiome in autoimmune hepatitis

Gut ◽

10.1136/gutjnl-2018-317836 ◽

2019 ◽

Vol 69 (3) ◽

pp. 569-577 ◽

Cited By ~ 27

Author(s):

Yiran Wei ◽

Yanmei Li ◽

Li Yan ◽

Chunyan Sun ◽

Qi Miao ◽

...

Keyword(s):

Autoimmune Hepatitis ◽

Gut Microbiome ◽

Alpha Diversity ◽

Disease Status ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Healthy Controls ◽

Microbial Composition ◽

Cross Sectional ◽

Treatment Naïve

ObjectiveThe significance of the liver-microbiome axis has been increasingly recognised as a major modulator of autoimmunity. The aim of this study was to take advantage of a large well-defined corticosteroids treatment-naïve group of patients with autoimmune hepatitis (AIH) to rigorously characterise gut dysbiosis compared with healthy controls.DesignWe performed a cross-sectional study of individuals with AIH (n=91) and matched healthy controls (n=98) by 16S rRNA gene sequencing. An independent cohort of 28 patients and 34 controls was analysed to validate the results. All the patients were collected before corticosteroids therapy.ResultsThe gut microbiome of steroid treatment-naïve AIH was characterised with lower alpha-diversity (Shannon and observed operational taxonomic units, both p<0.01) and distinct overall microbial composition compared with healthy controls (p=0.002). Depletion of obligate anaerobes and expansion of potential pathobionts including Veillonella were associated with disease status. Of note, Veillonella dispar, the most strongly disease-associated taxa (p=8.85E–8), positively correlated with serum level of aspartate aminotransferase and liver inflammation. Furthermore, the combination of four patients with AIH-associated genera distinguished AIH from controls with an area under curves of approximately 0.8 in both exploration and validation cohorts. In addition, multiple predicted functional modules were altered in the AIH gut microbiome, including lipopolysaccharide biosynthesis as well as metabolism of amino acids that can be processed by bacteria to produce immunomodulatory metabolites.ConclusionOur study establishes compositional and functional alterations of gut microbiome in AIH and suggests the potential for using gut microbiota as non-invasive biomarkers to assess disease activity.

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Effect of Selected Stilbenoids on Human Fecal Microbiota

Molecules ◽

10.3390/molecules24040744 ◽

2019 ◽

Vol 24 (4) ◽

pp. 744 ◽

Cited By ~ 6

Author(s):

Jose Jaimes ◽

Veronika Jarosova ◽

Ondrej Vesely ◽

Chahrazed Mekadim ◽

Jakub Mrazek ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Statistical Tests ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Microbial Composition ◽

Genus Clostridium ◽

The Family ◽

Rrna Gene Sequencing

Dietary phenolics or polyphenols are mostly metabolized by the human gut microbiota. These metabolites appear to confer the beneficial health effects attributed to phenolics. Microbial composition affects the type of metabolites produced. Reciprocally, phenolics modulate microbial composition. Understanding this relationship could be used to positively impact health by phenolic supplementation and thus create favorable colonic conditions. This study explored the effect of six stilbenoids (batatasin III, oxyresveratrol, piceatannol, pinostilbene, resveratrol, thunalbene) on the gut microbiota composition. Stilbenoids were anaerobically fermented with fecal bacteria from four donors, samples were collected at 0 and 24 h, and effects on the microbiota were assessed by 16S rRNA gene sequencing. Statistical tests identified affected microbes at three taxonomic levels. Observed microbial composition modulation by stilbenoids included a decrease in the Firmicutes to Bacteroidetes ratio, a decrease in the relative abundance of strains from the genus Clostridium, and effects on the family Lachnospiraceae. A frequently observed effect was a further decrease of the relative abundance when compared to the control. An opposite effect to the control was observed for Faecalibacterium prausnitzii, whose relative abundance increased. Observed effects were more frequently attributed to resveratrol and piceatannol, followed by thunalbene and batatasin III.

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