scholarly journals Wastewater treatment works change the intestinal microbiomes of insectivorous bats

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247475
Author(s):  
Calvin Mehl ◽  
M. Corrie Schoeman ◽  
Tomasz J. Sanko ◽  
Carlos Bezuidenhout ◽  
Charlotte M. S. Mienie ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Intestinal Microbiota ◽  
Intestinal Bacteria ◽  
Nutrient Content ◽  
Gene Profiling ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Reference Sites ◽  
Intrinsic Factors ◽  
Chironomid Midges

Mammals, born with a near-sterile intestinal tract, are inoculated with their mothers’ microbiome during birth. Thereafter, extrinsic and intrinsic factors shape their intestinal microbe assemblage. Wastewater treatment works (WWTW), sites synonymous with pollutants and pathogens, receive influent from domestic, agricultural and industrial sources. The high nutrient content of wastewater supports abundant populations of chironomid midges (Diptera), which transfer these toxicants and potential pathogens to their predators, such as the banana bat Neoromicia nana (Vespertilionidae), thereby influencing their intestinal microbial assemblages. We used next generation sequencing and 16S rRNA gene profiling to identify and compare intestinal bacteria of N. nana at two reference sites and two WWTW sites. We describe the shared intestinal microbiome of the insectivorous bat, N. nana, consisting of seven phyla and eleven classes. Further, multivariate analyses revealed that location was the most significant driver (sex, body size and condition were not significant) of intestinal microbiome diversity. Bats at WWTW sites exhibited greater intestinal microbiota diversity than those at reference sites, likely due to wastewater exposure, stress and/or altered diet. Changes in their intestinal microbiota assemblages may allow these bats to cope with concomitant stressors.

scholarly journals Pathogenetic Substantiation of the Therapeutic Impact on Microbiota in Irritable Bowel Syndrome

2019 ◽  
Vol 29 (4) ◽  
pp. 7-14
Author(s):  
Yu. O. Shulpekova ◽  
G. H. Babaeva ◽  
V. Yu. Rusyaev
Keyword(s):  
Irritable Bowel Syndrome ◽  
Intestinal Microbiota ◽  
Intestinal Bacteria ◽  
Host Cells ◽  
Intestinal Microbiome ◽  
Bacterial Strains ◽  
Blastocystis Hominis ◽  
Therapeutic Impact ◽  
Irritable Bowel ◽  
Positive Effect

Aim. This review aims to describe the nature of changes in the intestinal microbiota in irritable bowel syndrome (IBS) and provide a pathogenetic justification of the feasibility of a therapeutic impact on microbiota. General findings. An important aspect of the interaction of intestinal bacteria with the “host” cells is their contact with pattern recognition receptors of enterocytes, dendritic cell receptors, as well as a transcellular transport of antigens in the region of Peyer’s patches. The area of interaction of intestinal bacteria and the human body is not limited to the intestines. Intestinal bacteria demonstrate a significant humoral effect due to signalling molecules, some of which exhibit neurotransmitter properties. The study of the bacterial cross-feeding for various species, i.e. mutual use of nutrient substrates produced by bacteria of various species, is of a great interest. The development of a lowactivity inflammation in IBS can partly be explained by the increased interaction of flagellin with the corresponding receptor, as well as the influx of excess bacteria from the small intestine. The majority of studies on IBS have demonstrated the predominance of intestinal bacteria with pro-inflammatory potential (Enterobacteriaceae) and the lack of bacteria with a pronounced anti-inflammatory, antimicrobial and enzymatic action (Lactobacillus and Bifidobacterium), as well as increased mucus degradation. Similar changes are observed in inflammatory bowel diseases. Reduced microbial diversity increases susceptibility to intestinal infections and parasitoses, including those caused by protozoa conditionally pathogenic for adults, such as Blastocystis hominis hominis, Dientamoeba fragilis, Giardia lamblia. With the help of nutrition correction, the use of probiotics and functional foods containing certain probiotic strains, plant fibres (primarily psyllium) and, in some cases, nonabsorbable antibiotics, a positive effect can be achieved in a significant number of IBS patients. Recent works have shown that clinical improvement is accompanied by a change in the composition of the intestinal microbiota.Conclusion. For the pathogenetic treatment of irritable bowel syndrome, the use of non-drug treatment is justified, such as diet optimization and prescription of plant fibres and probiotic bacterial strains. The positive effect of such an approach is largely determined by modification of the intestinal microbiota composition. This opens up prospects for a further, more targeted impact on the intestinal microbiome.

scholarly journals Lyophilized Fecal Microbiota Transplantation Capsules for Recurrent Clostridium difficile Infection

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S381-S381
Author(s):  
Hebert Dupont ◽  
Zhi-Dong Jiang ◽  
Ashley Alexander ◽  
Nadim Ajami ◽  
Joseph F Petrosino ◽  
...  
Keyword(s):  
Oral Delivery ◽  
Fecal Microbiota Transplantation ◽  
Fecal Microbiota ◽  
Gene Profiling ◽  
Intestinal Microbiome ◽  
Published Data ◽  
Rrna Gene ◽  
Second Phase ◽  
Microbiome Diversity

Abstract Background Fecal microbiota (FM) transplantation (FMT) is a highly effective treatment of recurrent C. difficile infection (rCDI). We have published data showing efficacy of fresh, frozen and lyophilized donor microbiota administered by colonoscopy. Most groups are moving toward use of frozen product given by enema and in evaluating encapsulated product for oral delivery. Methods This was a prospective, randomized study of subjects with rCDI (≥ 3 episodes) treated with encapsulated lyophilized FM 100 g given once or 100 g given on two successive days (total 200 g) vs. frozen FM product 100 g given by single retention enema, between March 2015 and February 2017. The clinical outcome was absence of CDI during the 60 days after FMT. The subjects were followed for 6 months for safety. In a subset recipients, microbiome composition by 16S rRNA gene profiling were analyzed on stools obtained pre- and day 2, 7, 14, 30, 60 and 90 days after FMT. Results A total of 54 subjects were enrolled (37/54; 69% female) with a median age of 71 years (range: 20–97). In the first 14 subjects treated, cure rates for oral capsules 100 g FM was 5/8 (63%) vs. 6/6 (100%) for those receiving 100 g frozen FM by enema (P = 0.209). In the second phase of the study cure rate for oral capsules 200 g FM was 17/18 (91%) vs. 20/21 (94%) for the subjects treated by enema by 100 g of frozen product (P = 0.782). No side effects were felt to be related to the procedure or the FMT products were recorded during 6 months follow-up. Two subjects died during follow-up between 3 and 6 months after study due to underlying medical conditions felt to be unrelated to FMT. Microbiota analysis were performed on 40 subjects of which 19/40 (48%) had received capsules. Figure showed that restoration of the intestinal microbiome diversity and Taxa began apparent by 2 days after FMT in both groups and resembled the donor product by 2 weeks with stabilization of the microbiota diversity and Taxa persisting for the 90 days of observation. Conclusion Administration of encapsulated, lyophilized FM resulted in durable restoration of intestinal microbiome diversity comparable to results seen with frozen product given by enema. Disclosures All authors: No reported disclosures.

scholarly journals Impact of Antibiotic Gut Exposure on the Temporal Changes in Microbiome Diversity

2019 ◽  
Vol 63 (10) ◽  
Author(s):  
Charles Burdet ◽  
Thu Thuy Nguyen ◽  
Xavier Duval ◽  
Stéphanie Ferreira ◽  
Antoine Andremont ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Day Treatment ◽  
Temporal Changes ◽  
Shannon Index ◽  
Gene Profiling ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Mixed Effect

ABSTRACT Although the global deleterious impact of antibiotics on the intestinal microbiota is well known, temporal changes in microbial diversity during and after an antibiotic treatment are still poorly characterized. We used plasma and fecal samples collected frequently during treatment and up to one month after from 22 healthy volunteers assigned to a 5-day treatment by moxifloxacin (n = 14) or no intervention (n = 8). Moxifloxacin concentrations were measured in both plasma and feces, and bacterial diversity was determined in feces by 16S rRNA gene profiling and quantified using the Shannon index and number of operational taxonomic units (OTUs). Nonlinear mixed effect models were used to relate drug pharmacokinetics and bacterial diversity over time. Moxifloxacin reduced bacterial diversity in a concentration-dependent manner, with a median maximal loss of 27.5% of the Shannon index (minimum [min], 17.5; maximum [max], 27.7) and 47.4% of the number of OTUs (min, 30.4; max, 48.3). As a consequence of both the long fecal half-life of moxifloxacin and the susceptibility of the gut microbiota to moxifloxacin, bacterial diversity indices did not return to their pretreatment levels until days 16 and 21, respectively. Finally, the model characterized the effect of moxifloxacin on bacterial diversity biomarkers and provides a novel framework for analyzing antibiotic effects on the intestinal microbiome.

scholarly journals Movement and Fixation of Intestinal Microbiota after Administration of Human Feces to Germfree Mice

2005 ◽  
Vol 71 (6) ◽  
pp. 3171-3178 ◽  
Author(s):  
Ryoko Kibe ◽  
Mitsuo Sakamoto ◽  
Hiroshi Yokota ◽  
Hiroki Ishikawa ◽  
Yuji Aiba ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Intestinal Bacteria ◽  
Rrna Gene ◽  
Culture Methods ◽  
Total Peak Area ◽  
Human Intestinal Microbiota ◽  
Human Intestinal Bacteria ◽  
The Family ◽  
Mouse Intestine ◽  
Human Flora

ABSTRACT Human flora-associated (HFA) mice have been considered a tool for studying the ecology and metabolism of intestinal bacteria in humans, although they have some limitations as a model. Shifts in dominant species of microbiota in HFA mice after the administration of human intestinal microbiota was revealed by 16S rRNA gene sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses. Characteristic terminal restriction fragments (T-RFs) were quantified as the proportion of total peak area of all T-RFs. Only the proportion of the T-RF peak at bp 366, identified as the Gammmaproteobacteria group and the family Coriobacteriaceae, was reduced in this study. Increased T-RFs over time at bp 56, 184, and 196 were affiliated with the Clostridium group. However, most of the isolated bacteria with unique population shifts were phylotypes. The vertical transmission of the intestinal microbiota of the mouse offspring was also investigated by dendrogram analysis derived from the similarity of T-RFLP patterns among samples. As a result, the intestinal microbiota of HFA mice and their offspring reflected the composition of individual human intestinal bacteria with some modifications. Moreover, we revealed that human-derived lactobacilli (HDL), which have been considered difficult to colonize in the HFA mouse intestine in previous studies based on culture methods, could be detected in the HFA mouse intestine by using a lactic acid bacterium-specific primer and HDL-specific primers. Our results indicate that the intestinal microbiota of HFA mice represents a limited sample of bacteria from the human source and are selected by unknown interactions between the host and bacteria.

scholarly journals Multivariate Analysis in Microbiome Description: Correlation of Human Gut Protein Degraders, Metabolites, and Predicted Metabolic Functions

2021 ◽  
Vol 12 ◽  
Author(s):  
Stefano Raimondi ◽  
Rosalba Calvini ◽  
Francesco Candeliere ◽  
Alan Leonardi ◽  
Alessandro Ulrici ◽  
...  
Keyword(s):  
Intestinal Bacteria ◽  
Fecal Microbiota ◽  
Sensu Stricto ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Metabolic Functions ◽  
Genes Encoding ◽  
The Face ◽  
Microbiome Data

Protein catabolism by intestinal bacteria is infamous for releasing many harmful compounds, negatively affecting the health status, both locally and systemically. In a previous study, we enriched in protein degraders the fecal microbiota of five subjects, utilizing a medium containing protein and peptides as sole fermentable substrates and we monitored their evolution by 16S rRNA gene profiling. In the present study, we fused the microbiome data and the data obtained by the analysis of the volatile organic compounds (VOCs) in the headspace of the cultures. Then, we utilized ANOVA simultaneous component analysis (ASCA) to establish a relationship between metabolites and bacteria. In particular, ASCA allowed to separately assess the effect of subject, time, inoculum concentration, and their binary interactions on both microbiome and volatilome data. All the ASCA submodels pointed out a consistent association between indole and Escherichia–Shigella, and the relationship of butyric, 3-methyl butanoic, and benzenepropanoic acids with some bacterial taxa that were major determinants of cultures at 6 h, such as Lachnoclostridiaceae (Lachnoclostridium), Clostridiaceae (Clostridium sensu stricto), and Sutterellaceae (Sutterella and Parasutterella). The metagenome reconstruction with PICRUSt2 and its functional annotation indicated that enrichment in a protein-based medium affected the richness and diversity of functional profiles, in the face of a decrease of richness and evenness of the microbial community. Linear discriminant analysis (LDA) effect size indicated a positive differential abundance (p < 0.05) for the modules of amino acid catabolism that may be at the basis of the changes of VOC profile. In particular, predicted genes encoding functions belonging to the superpathways of ornithine, arginine, and putrescine transformation to GABA and eventually to succinyl-CoA, of methionine degradation, and various routes of breakdown of aromatic compounds yielding succinyl-CoA or acetyl-CoA became significantly more abundant in the metagenome of the bacterial community.

scholarly journals Antimicrobial resistance gene surveillance in the receiving waters of an upgraded wastewater treatment plant

FACETS ◽  
2018 ◽  
Vol 3 (1) ◽  
pp. 128-138 ◽  
Author(s):  
Claire N. Freeman ◽  
Lena Scriver ◽  
Kara D. Neudorf ◽  
Lisbeth Truelstrup Hansen ◽  
Rob C. Jamieson ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Antimicrobial Resistance ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Nutrient Content ◽  
Rrna Gene ◽  
Treated Effluent ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
The Impact

Wastewater treatment plants (WWTPs) have been identified as hotspots for antimicrobial resistance genes (ARGs) and thus represent a critical point where patterns in ARG abundances can be monitored prior to their release into the environment. The aim of the current study was to measure the impact of the release of the final treated effluent (FE) on the abundance of ARGs in the receiving water of a recently upgraded WWTP in the Canadian prairies. Sample nutrient content (phosphorous and nitrogen species) was measured as a proxy for WWTP functional performance, and quantitative PCR (qPCR) was used to measure the abundance of eight ARGs, the intI1 gene associated with class I integrons, and the 16S rRNA gene. The genes ermB, sul1, intI1, blaCTX-M, qnrS, and tetO all had higher abundances downstream of the WWTP, consistent with the genes with highest abundance in the FE. These findings are consistent with the increasing evidence suggesting that human activity affects the abundances of ARGs in the environment. Although the degree of risk associated with releasing ARGs into the environment is still unclear, understanding the environmental dimension of this threat will help develop informed management policies to reduce the spread of antibiotic resistance and protect public health.

scholarly journals Role of the Intestinal Microbiome, Intestinal Barrier and Psychobiotics in Depression

Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 927
Author(s):  
Paulina Trzeciak ◽  
Mariola Herbet
Keyword(s):  
Immune System ◽  
Intestinal Microbiota ◽  
Intestinal Barrier ◽  
Intestinal Bacteria ◽  
Intestinal Microbiome ◽  
Stress Reactions ◽  
Treatment Of Depression ◽  
Increased Activity ◽  
Excessive Activation

The intestinal microbiota plays an important role in the pathophysiology of depression. As determined, the microbiota influences the shaping and modulation of the functioning of the gut–brain axis. The intestinal microbiota has a significant impact on processes related to neurotransmitter synthesis, the myelination of neurons in the prefrontal cortex, and is also involved in the development of the amygdala and hippocampus. Intestinal bacteria are also a source of vitamins, the deficiency of which is believed to be related to the response to antidepressant therapy and may lead to exacerbation of depressive symptoms. Additionally, it is known that, in periods of excessive activation of stress reactions, the immune system also plays an important role, negatively affecting the tightness of the intestinal barrier and intestinal microflora. In this review, we have summarized the role of the gut microbiota, its metabolites, and diet in susceptibility to depression. We also describe abnormalities in the functioning of the intestinal barrier caused by increased activity of the immune system in response to stressors. Moreover, the presented study discusses the role of psychobiotics in the prevention and treatment of depression through their influence on the intestinal barrier, immune processes, and functioning of the nervous system.

scholarly journals Ceftriaxone and Cefotaxime Have Similar Effects on the Intestinal Microbiota in Human Volunteers Treated by Standard-Dose Regimens

2019 ◽  
Vol 63 (6) ◽  
Author(s):  
Charles Burdet ◽  
Nathalie Grall ◽  
Morgane Linard ◽  
Antoine Bridier-Nahmias ◽  
Michèle Benhayoun ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Intestinal Microbiota ◽  
Standard Dose ◽  
Generation Cephalosporin ◽  
Gene Profiling ◽  
Pharmacokinetic Analysis ◽  
Rrna Gene ◽  
Open Label ◽  
Gram Negative ◽  
Human Volunteers

ABSTRACT Ceftriaxone has a higher biliary elimination than cefotaxime (40% versus 10%), which may result in a more pronounced impact on the intestinal microbiota. We performed a monocenter, randomized open-label clinical trial in 22 healthy volunteers treated by intravenous ceftriaxone (1 g/24 h) or cefotaxime (1 g/8 h) for 3 days. We collected fecal samples for phenotypic analyses, 16S rRNA gene profiling, and measurement of the antibiotic concentration and compared the groups for the evolution of microbial counts and indices of bacterial diversity over time. Plasma samples were drawn at day 3 for pharmacokinetic analysis. The emergence of 3rd-generation-cephalosporin-resistant Gram-negative enteric bacilli (Enterobacterales), Enterococcus spp., or noncommensal microorganisms was not significantly different between the groups. Both antibiotics reduced the counts of total Gram-negative enteric bacilli and decreased the bacterial diversity, but the differences between the groups were not significant. All but one volunteer from each group exhibited undetectable levels of antibiotic in feces. Plasma pharmacokinetic endpoints were not correlated to alteration of the bacterial diversity of the gut. Both antibiotics markedly impacted the intestinal microbiota, but no significant differences were detected when standard clinical doses were administered for 3 days. This might be related to the similar daily amounts of antibiotics excreted through the bile using a clinical regimen. (This study has been registered at ClinicalTrials.gov under identifier NCT02659033.)

scholarly journals Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding

2018 ◽  
Author(s):  
Milica Ciric ◽  
David Waite ◽  
Jenny Draper ◽  
John Brian Jones
Keyword(s):  
Gut Microbiota ◽  
Heat Wave ◽  
Intestinal Microbiota ◽  
Chinook Salmon ◽  
Intestinal Flora ◽  
Intestinal Content ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Summer Heat

ABSTRACTWith the growing importance of aquaculture worldwide, characterisation of the microbial flora of high-value aquaculture species and identification of gut flora shifts induced by changes in fish physiology or nutrition is of special interest.Here we report the first metabarcoding survey of the intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and intestinal samples, and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles.Over 1,000 operational taxonomic units (OTUs) were identified within the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae.This survey was performed amid a summer heat wave, during which the fish exhibited reduced feeding. Although the sampled fish appeared healthy, they had minimal intestinal content, and the observed intestinal flora may represent the microbiota of fasting and stressed fish. Limited comparison between Mycoplasma and Vibrio sequences from the Chinook salmon gut and published microbial sequences from the intestines of a variety of fish species (including Atlantic salmon) indicated that despite the starvation and temperature variations, the replacement of Vibrio with Mycoplasma is occurring within expected ecological parameters and does not necessarily reflect colonisation by atypical microbes.DATA SUMMARYRaw sequences from Chinook salmon intestinal microbiome 16S survey generated on the Illumina platform are publically available through NCBI Sequence Read Archive (SRA) database:Bioproject PRJNA421844SRA study SRP134829https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421844IMPACT STATEMENTAlthough 16S metabarcoding surveys are becoming routine, little is still known about the microbiota of fish. This is the first survey of the intestinal microbiota of Chinook salmon, a species native to the Pacific Northwest which is farmed in New Zealand and Chile. While most intestinal microbiota studies are performed on faecal material, we directly sampled the intestine epithelium and content.During the time of sampling, the farmed fish population was experiencing stress from a summer heat wave and had little intestinal content. Over 1,000 operational taxonomic units (OTUs) were identified within the intestines of the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon.We believe this survey will be of interest not only to those interested in fish biology and aquaculture, but also as an addition to the ongoing debate in the literature on sampling and DNA extraction methods for challenging samples.

scholarly journals Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

2021 ◽  
Vol 44 (2) ◽  
Author(s):  
Jumria Sutra ◽  
Hamidu Saadu ◽  
Amalia Mohd. Hashim ◽  
Mohd Zamri Saad ◽  
Ina Salwany Md Yasin ◽  
...  
Keyword(s):  
Information Processing ◽  
Intestinal Microbiota ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Intestinal Microbiome ◽  
Functional Genes ◽  
Rrna Gene ◽  
Wet Season ◽  
Asian Seabass ◽  
Tiger Grouper

Grouper and Asian seabass are among the economically important cultured marine fish in Malaysia. However, fry productions in large scale tend to introduce stress that changes the fish microbiota and increases susceptibility to diseases. Currently, high-throughput sequencing is used to study fish microbiota and their respective gene functions. In this study, we investigate the diversity, abundance and functional genes of intestinal microbiota of tiger grouper and Asian seabass that were reared in a semi-closed hatchery during dry and wet seasons. Intestinal samples were collected from tiger grouper and Asian seabass of different sizes before proceeded to DNA extraction. The extracted DNA were then subjected to 16S rRNA gene amplicon sequencing using the Illumina Miseq platform targeting V3 and V4 regions for determination of the bacterial diversity, abundance and functional genes in both seasons. The results revealed that intestinal microbiota of Asian seabass were dominated by the phylum Proteobacteria and order Vibrionales in both seasons. Meanwhile, intestinal microbiome of tiger groupers were shifted from domination of phylum Firmicutes and order Clostridiales in dry season to Proteobacteria and order Lactobacillales in wet season. PICRUSt analysis revealed that the functional genes that were dominantly present were the genes encoded for metabolism, genetic information processing, environmental information processing, cellular process and human diseases. Remarkably, SIMPER analysis showed several potential metagenomics biomarker genes in dry and wet seasons. This study revealed the importance of utilizing amplicon metagenomics approaches in microbiome studies for better identification of the microbial profiling in aquaculture systems.

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