Effects of Vibrio cholerae infection and colonization on the zebrafish intestinal microbiome

Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic, and can be significantly altered to due external factors. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae needs to colonize the intestine of an exposed host for any type of pathogenicity to occur. It is suspected that members of the resident intestinal microbial community need to be eliminated by V. cholerae in order for colonization, and subsequently disease, to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal community. In this study, 16S rRNA gene sequencing was utilized to investigate how various strains of V. cholerae alter the aforementioned microbial profiles following an infection. We found that V. cholerae infection and subsequent colonization induced significant changes in the zebrafish intestinal microbiome, with specific members of the microbial community targeted. Additional salient differences to the microbial profile were observed based on the particular strain of V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae causes significant modulation to the zebrafish intestinal microbiome in order for infection and subsequent disease to occur.

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Vibrio cholerae Infection Induces Strain Specific Modulation of the Zebrafish Intestinal Microbiome

Infection and Immunity ◽

10.1128/iai.00157-21 ◽

2021 ◽

Author(s):

Paul Breen ◽

Andrew D. Winters ◽

Kevin R. Theis ◽

Jeffrey H. Withey

Keyword(s):

Vibrio Cholerae ◽

Model Organism ◽

16S Rrna Gene Sequencing ◽

Intestinal Microbiome ◽

Model Organisms ◽

Rrna Gene ◽

Microbial Profile ◽

Aquatic Microbes ◽

Host Microbe Interactions ◽

Rrna Gene Sequencing

Zebrafish ( Danio rerio ) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. Zebrafish contain a core ( i.e. , consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic, and can be significantly altered to due external factors. Zebrafish are particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae . As an intestinal pathogen, V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. Members of the resident intestinal microbial community likely must be reduced or eliminated by V. cholerae in order for colonization, and subsequent disease, to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few have examined how a V. cholerae infection alters the resident intestinal microbiome. In this study, 16S rRNA gene sequencing was utilized to investigate how five genetically diverse V. cholerae strains alter the intestinal microbiome following an infection. We found that V. cholerae colonization induced significant changes in the zebrafish intestinal microbiome. Notably, changes in the microbial profile were significantly different from each other, based on the particular strain of V. cholerae used to infect zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiota to enable colonization and specific microbes that are targeted depend on the V. cholerae genotype.

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The Vibrio cholerae T6SS is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome

Infection and Immunity ◽

10.1128/iai.00151-21 ◽

2021 ◽

Author(s):

Paul Breen ◽

Andrew D. Winters ◽

Kevin R. Theis ◽

Jeffrey H. Withey

Keyword(s):

Vibrio Cholerae ◽

Model Organism ◽

16S Rrna Gene Sequencing ◽

Intestinal Microbiome ◽

Model Organisms ◽

Rrna Gene ◽

Composition And Structure ◽

Aquatic Microbes ◽

Host Microbe Interactions ◽

Rrna Gene Sequencing

Zebrafish ( Danio rerio ) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae , an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was essential for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.

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Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses

Scientific Reports ◽

10.1038/s41598-019-49365-w ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Zhou Jiang ◽

Ping Li ◽

Yanhong Wang ◽

Han Liu ◽

Dazhun Wei ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Arsenic Mobilization ◽

Rrna Gene Sequencing ◽

High Arsenic ◽

High Arsenic Groundwater

Abstract Microbial metabolisms of arsenic, iron, sulfur, nitrogen and organic matter play important roles in arsenic mobilization in aquifer. In this study, microbial community composition and functional potentials in a high arsenic groundwater were investigated using integrated techniques of RNA- and DNA-based 16S rRNA gene sequencing, metagenomic sequencing and functional gene arrays. 16S rRNA gene sequencing showed the sample was dominated by members of Proteobacteria (62.3–75.2%), such as genera of Simplicispira (5.7–6.7%), Pseudomonas (3.3–5.7%), Ferribacterium (1.6–4.4%), Solimonas (1.8–3.2%), Geobacter (0.8–2.2%) and Sediminibacterium (0.6–2.4%). Functional potential analyses indicated that organics degradation, assimilatory sulfate reduction, As-resistant pathway, iron reduction, ammonification, nitrogen fixation, denitrification and dissimilatory nitrate reduction to ammonia were prevalent. The composition and function of microbial community and reconstructed genome bins suggest that high level of arsenite in the groundwater may be attributed to arsenate release from iron oxides reductive dissolution by the iron-reducing bacteria, and subsequent arsenate reduction by ammonia-producing bacteria featuring ars operon. This study highlights the relationship between biogeochemical cycling of arsenic and nitrogen in groundwater, which potentially occur in other aquifers with high levels of ammonia and arsenic.

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Changes in the Intestinal Microbiome during a Multispecies Probiotic Intervention in Compensated Cirrhosis

Nutrients ◽

10.3390/nu12061874 ◽

2020 ◽

Vol 12 (6) ◽

pp. 1874 ◽

Cited By ~ 1

Author(s):

Angela Horvath ◽

Marija Durdevic ◽

Bettina Leber ◽

Katharina di Vora ◽

Florian Rainer ◽

...

Keyword(s):

Gut Microbiome ◽

Controlled Trial ◽

16S Rrna Gene Sequencing ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Microbiome Composition ◽

Beneficial Effects ◽

Compensated Cirrhosis ◽

Gut Barrier Function ◽

Probiotic Treatment

Probiotics have been used in trials to therapeutically modulate the gut microbiome and have shown beneficial effects in cirrhosis. However, their effect on the microbiome of cirrhosis patients is not fully understood yet. Here, we tested the effects of a multispecies probiotic on microbiome composition in compensated cirrhosis. The gut microbiome composition of 58 patients with compensated cirrhosis from a randomized controlled trial who received a daily dose of multispecies probiotics or placebo for six months was analysed by 16S rRNA gene sequencing. Microbiome composition of patients who received probiotics was enriched with probiotic strains and the abundance of Faecalibacterium prausnitzii, Syntrophococcus sucromutans, Bacteroides vulgatus, Alistipes shahii and a Prevotella species was increased in the probiotic group compared to the placebo group. Patients who had microbiome changes in response to probiotic treatment also showed a significant increase in neopterin and a significant decrease in faecal zonulin levels after intervention, which was not observed in placebo-treated patients or patients with unchanged microbiome compositions. In conclusion, multispecies probiotics may enrich the microbiome of compensated cirrhotic patients with probiotic bacteria during a six-month intervention and beneficially change the residential microbiome and gut barrier function.

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Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

The Journals of Gerontology Series A ◽

10.1093/gerona/glaa256 ◽

2020 ◽

Author(s):

Ravichandra Vemuri ◽

Chrissy Sherrill ◽

Matthew A Davis ◽

Kylie Kavanagh

Keyword(s):

Microbial Community ◽

Systemic Inflammation ◽

16S Rrna Gene Sequencing ◽

Microbial Interactions ◽

Rrna Gene ◽

Vervet Monkeys ◽

Fecal Samples ◽

Age Related ◽

Rrna Gene Sequencing ◽

The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

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Early-Life Intake of an Isotonic Protein Drink Improves the Gut Microbial Profile of Piglets

Animals ◽

10.3390/ani10050879 ◽

2020 ◽

Vol 10 (5) ◽

pp. 879

Author(s):

Stefan G. Buzoianu ◽

Ava M. Firth ◽

CallaBria Putrino ◽

Fabio Vannucci

Keyword(s):

Environmental Changes ◽

16S Rrna Gene Sequencing ◽

Control Group ◽

Rrna Gene ◽

Bacterial Populations ◽

E Coli ◽

Microbial Profile ◽

Before And After ◽

Potential Alternative ◽

Rrna Gene Sequencing

A healthy microbial community in the gut of piglets is critical to minimize the negative performance consequences associated with dietary and environmental changes that occur at weaning. Tonisity Px, an isotonic protein drink, is a potential alternative to balance the gut microbiota as it contains key ingredients for nourishing the small intestine. In the present study, 16 litters comprising 161 piglets were randomly allocated to a group to which Tonisity Px was provided from days 2 to 8 of age (TPX group) or to a control group, to which no Tonisity Px was provided. The TPX group also received Tonisity Px in the 3 days before and after weaning. At days 9, 17, and 30 of age, fecal and ileum samples were collected from piglets belonging to both groups and analyzed using 16S rRNA gene sequencing, semiquantitative PCR of Rotavirus serogroups, and semiquantitative Escherichia coli culture. Overall, Tonisity Px increased the abundance of beneficial bacterial populations (Lactobacillus and Bacteroides species) and reduced potentially pathogenic bacterial populations (E. coli and Prevotellaceae), in both the pre-weaning and post-weaning periods.

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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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High-throughput 16S rRNA gene sequencing of the microbial community associated with palm oil mill effluents of two oil processing systems

Scientific Reports ◽

10.1038/s41598-021-92513-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Benedicte Ella Zranseu Aka ◽

Theodore N’dede Djeni ◽

Simon Laurent Tiemele Amoikon ◽

Jan Kannengiesser ◽

Naaila Ouazzani ◽

...

Keyword(s):

Microbial Community ◽

Palm Oil ◽

Microbial Community Composition ◽

16S Rrna Gene Sequencing ◽

Illumina Miseq ◽

Rrna Gene ◽

Industrial Plants ◽

Oil Processing ◽

Microbial Contaminants ◽

Palm Oil Mill

AbstractPalm Oil Mill Effluents (POME) are complex fermentative substrates which habour diverse native microbial contaminants. However, knowledge on the microbiota community shift caused by the anthropogenic effects of POME in the environment is up to date still to be extensively documented. In this study, the bacterial and archaeal communities of POME from two palm oil processing systems (artisanal and industrial) were investigated by Illumina MiSeq Platform. Despite the common characteristics of these wastewaters, we found that their microbial communities were significantly different with regard to their diversity and relative abundance of their different Amplicon Sequence Variants (ASV). Indeed, POME from industrial plants harboured as dominant phyla Firmicutes (46.24%), Bacteroidetes (34.19%), Proteobacteria (15.11%), with the particular presence of Spirochaetes, verrucomicrobia and Synergistetes, while those from artisanal production were colonized by Firmicutes (92.06%), Proteobacteria (4.21%) and Actinobacteria (2.09%). Furthermore, 43 AVSs of archaea were detected only in POME from industrial plants and assigned to Crenarchaeota, Diapherotrites, Euryarchaeota and Nanoarchaeaeota phyla, populated mainly by many methane-forming archaea. Definitively, the microbial community composition of POME from both type of processing was markedly different, showing that the history of these ecosystems and various processing conditions have a great impact on each microbial community structure and diversity. By improving knowledge about this microbiome, the results also provide insight into the potential microbial contaminants of soils and rivers receiving these wastewaters.

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First-in-class microbial ecosystem therapeutics 4 (MET4) in metastatic solid cancer patients treated with immunotherapy: MET4-IO.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.3098 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 3098-3098 ◽

Cited By ~ 1

Author(s):

Daniel Vilarim Araujo ◽

Marc Oliva Bernal ◽

Tira Jing Ying Tan ◽

Alya Abbas Heirali ◽

Pierre H.H. Schneeberger ◽

...

Keyword(s):

Cancer Patients ◽

16S Rrna Gene Sequencing ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Solid Cancer ◽

Fecal Transplant ◽

Additional Time ◽

Microbial Ecosystem ◽

Shannon Diversity ◽

To Receive

3098 Background: Therapeutic augmentation of the intestinal microbiome to improve immunotherapy outcomes is an active area of investigation. Microbial Ecosystem Therapeutics (METs) are consortia of human-derived bacteria designed to be reproducible, scalable and safe alternatives to fecal transplant. MET4 is a first-in-class consortium of taxa associated with immune checkpoint inhibitor (ICI)-responsiveness. Here we describe preliminary results of MET4-IO, an interventional trial assessing the safety and ecological effects of MET4 in ICI recipients. Methods: MET4-IO is a randomized investigator-initiated trial, evaluating MET4 in solid cancer patients treated with ICI. MET4-IO involves 3 cohorts of 65 total patients: Group A, a safety cohort of 5 patients already on ICI; Group B, patients starting ICI, randomized 3:1 to receive MET4 or not; Group C, patients on ICI who experience radiological progression but not clinical deterioration, randomized 1:1 to receive MET4 or not. Stool and blood samples are collected at baseline and 4-5 additional time-points. For this interim analysis, 16S rRNA gene sequencing was performed on fecal specimens. Shannon diversity, relative abundance (RA), number and fold-change of MET4 taxa > RA 0.01 were assessed and compared to controls. Results: As of January 26, 2020, 21 patients were enrolled (A = 5,B = 12,C = 4), and 15 (71%) received MET4. The mean age was 65.9 years, 40% were females, 52% had head and neck cancer and 19% melanoma. Sixteen patients (76%) were treated with an anti-PD1 agent as monotherapy and 5 with a combination of anti-PD1 and anti-CTLA4 antibodies. G3-4 toxicities (CTCAEv5.0) attributed to ICI were observed in 13% vs. 17% of MET4 exposed and control patients, respectively. Three patients (20%) experienced toxicities attributed to MET4, all grade 1 except G2 dyspepsia in 1 patient. A greater number of MET4-associated taxa were detectable in MET4 recipients than controls (p < 0.01), with a trend towards higher cumulative RA (p = 0.10). No significant change in Shannon diversity after MET4 was observed, however controls were more likely to lose diversity overtime than MET4 recipients (p = 0.05). Colonization with MET4 varied by recipient and by taxon. Bifidobacterium, Collinsella and Enterococcus were significantly more common and abundant in MET4 recipients than controls. Conclusions: In this cohort, MET4 treatment was safe and associated with higher MET4-associated taxa in recipients than controls. Further analyses including peripheral blood immunophenotyping are ongoing. Clinical trial information: NCT03686202 .

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The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis

BioMed Research International ◽

10.1155/2016/3241529 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 18

Author(s):

Wei Song ◽

Lingzhi Li ◽

Hongliang Huang ◽

Keji Jiang ◽

Fengying Zhang ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Antarctic Fish ◽

16S Rrna Gene Sequencing ◽

Physiological Characteristics ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera. The number of common OTUs (operational taxonomic units) varied from 346 to 768, while unique OTUs varied from 84 to 694 in the four species of Antarctic fish. Moreover, intestinal bacterial communities in individuals of each species were not really similar, and those in the four species were not absolutely different, suggesting that bacterial communities might influence the physiological characteristics of Antarctic fish, and the common bacterial communities might contribute to the fish survival ability in extreme Antarctic environment, while the different ones were related to the living habits. All of these results could offer certain information for the future study of Antarctic fish physiological characteristics.

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