scholarly journals The skin microbiome of cow-nose rays (Rhinoptera bonasus) in an aquarium touch-tank exhibit

2016 ◽  
Author(s):  
Patrick J Kearns ◽  
Jennifer L Bowen ◽  
Michael F Tlusty
Keyword(s):  
Microbial Community ◽  
New England ◽  
High Throughput Sequencing ◽  
Ventral Surface ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Microbial Composition ◽  
Human Interactions ◽  
Rhinoptera Bonasus ◽  
Public Aquarium

Public aquarium exhibits offer numerous educational opportunities for visitors while touch tank exhibits offer guests the ability to directly interact with marine life. However, despite the popularity of these exhibits, the effect of human interactions on the host-associated microbiome or the habitat microbiome remains unclear. Microbial communities, both host-associated and habitat associated can have great implications for host health and habitat function. To better understand the link between human interactions and the microbiome of a touch tank we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial community on the dorsal and ventral surfaces of cow-nose rays (Rhinoptera bonasus) as well as its environment in a frequently visited touch tank exhibit at the New England Aquarium. Our analyses revealed a distinct microbial community associated with the skin of the ray that had lower diversity than the surrounding habitat. The ray skin was dominated by three orders: Burkholderiales (~55%), Flavobacteriales (~19%) and Pseudomonadales (~12%), suggesting a potentially important role of these taxa in ray health. Further, there was no difference between dorsal and ventral surface of the ray in terms of microbial composition or diversity, and a very low presence of common human-associated microbial taxa (<1.5%). Our results suggest that human contact has a minimal effect on the skin and habitat microbiome of the cow-nose ray and that the ray skin harbors a distinct and lower diversity microbial community than its environment.

scholarly journals The skin microbiome of cow-nose rays (Rhinoptera bonasus) in an aquarium touch-tank exhibit

2016 ◽  
Author(s):  
Patrick J Kearns ◽  
Jennifer L Bowen ◽  
Michael F Tlusty
Keyword(s):  
Microbial Community ◽  
New England ◽  
High Throughput Sequencing ◽  
Ventral Surface ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Microbial Composition ◽  
Human Interactions ◽  
Rhinoptera Bonasus ◽  
Public Aquarium

Public aquarium exhibits offer numerous educational opportunities for visitors while touch tank exhibits offer guests the ability to directly interact with marine life. However, despite the popularity of these exhibits, the effect of human interactions on the host-associated microbiome or the habitat microbiome remains unclear. Microbial communities, both host-associated and habitat associated can have great implications for host health and habitat function. To better understand the link between human interactions and the microbiome of a touch tank we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial community on the dorsal and ventral surfaces of cow-nose rays (Rhinoptera bonasus) as well as its environment in a frequently visited touch tank exhibit at the New England Aquarium. Our analyses revealed a distinct microbial community associated with the skin of the ray that had lower diversity than the surrounding habitat. The ray skin was dominated by three orders: Burkholderiales (~55%), Flavobacteriales (~19%) and Pseudomonadales (~12%), suggesting a potentially important role of these taxa in ray health. Further, there was no difference between dorsal and ventral surface of the ray in terms of microbial composition or diversity, and a very low presence of common human-associated microbial taxa (<1.5%). Our results suggest that human contact has a minimal effect on the skin and habitat microbiome of the cow-nose ray and that the ray skin harbors a distinct and lower diversity microbial community than its environment.

scholarly journals Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1433
Author(s):  
Michele Berlanda ◽  
Giada Innocente ◽  
Barbara Simionati ◽  
Barbara Di Camillo ◽  
Sonia Facchin ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Dietary Intervention ◽  
Oral Treatment ◽  
Microbial Evolution ◽  
Rrna Gene ◽  
Gut Health ◽  
Microbial Composition ◽  
Chronic Enteropathies ◽  
Faecal Microbiome

Chronic enteropathies (CE) are gastrointestinal diseases that afflict about one in five dogs in Europe. Conventional therapeutic approaches include dietary intervention, pharmacological treatment and probiotic supplements. The patient response can be highly variable and the interventions are often not resolutive. Moreover, the therapeutic strategy is usually planned (and gradually corrected) based on the patient’s response to empirical treatment, with few indirect gut health indicators useful to drive clinicians’ decisions. The ever-diminishing cost of high-throughput sequencing (HTS) allows clinicians to directly follow and characterise the evolution of the whole gut microbial community in order to highlight possible weaknesses. In this framework, faecal microbiome transplantation (FMT) is emerging as a feasible solution to CE, based on the implant of a balanced, eubiotic microbial community from a healthy donor to a dysbiotic patient. In this study, we report the promising results of FMT carried out in a 9-year-old dog suffering from CE for the last 3 years. The patient underwent a two-cycle oral treatment of FMT and the microbiota evolution was monitored by 16S rRNA gene sequencing both prior to FMT and after the two administrations. We evaluated the variation of microbial composition by calculating three different alpha diversity indices and compared the patient and donor data to a healthy control population of 94 dogs. After FMT, the patient’s microbiome and clinical parameters gradually shifted to values similar to those observed in healthy dogs. Symptoms disappeared during a follow-up period of six months after the second FMT. We believe that this study opens the door for potential applications of FMT in clinical veterinary practice and highlights the need to improve our knowledge on this relevant topic.

scholarly journals Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristofer M. Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
Microbial Community ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Gram Positive Bacteria ◽  
Rigorous Framework ◽  
The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1492 ◽  
Author(s):  
Ben J. Callahan ◽  
Kris Sankaran ◽  
Julia A. Fukuyama ◽  
Paul J. McMurdie ◽  
Susan P. Holmes
Keyword(s):  
High Throughput Sequencing ◽  
Linear Models ◽  
Reference Database ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Nonparametric Testing ◽  
Abundance Estimates ◽  
Taxonomic Markers ◽  
Microbiome Data ◽  
Microbiome Data Analysis

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

scholarly journals Effect of Pyroligneous Acid on the Microbial Community Composition and Plant Growth-Promoting Bacteria (PGPB) in Soils

Soil Systems ◽  
2022 ◽  
Vol 6 (1) ◽  
pp. 10
Author(s):  
Anithadevi Kenday Sivaram ◽  
Logeshwaran Panneerselvan ◽  
Kannappar Mukunthan ◽  
Mallavarapu Megharaj
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Microbial Diversity ◽  
Growth And Yield ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Microbial Composition ◽  
Pyroligneous Acid ◽  
Plant Growth Promoting ◽  
Growth Promoting

Pyroligneous acid (PA) is often used in agriculture as a plant growth and yield enhancer. However, the influence of PA application on soil microorganisms is not often studied. Therefore, in this study, we investigated the effect of PA (0.01–5% w/w in soil) on the microbial diversity in two different soils. At the end of eight weeks of incubation, soil microbial community dynamics were determined by Illumina-MiSeq sequencing of 16S rRNA gene amplicons. The microbial composition differed between the lower (0.01% and 0.1%) and the higher (1% and 5%) concentration in both PA spiked soils. The lower concentration of PA resulted in higher microbial diversity and dehydrogenase activity (DHA) compared to the un-spiked control and the soil spiked with high PA concentrations. Interestingly, PA-induced plant growth-promoting bacterial (PGPB) genera include Bradyrhizobium, Azospirillum, Pseudomonas, Mesorhizobium, Rhizobium, Herbaspiriluum, Acetobacter, Beijerinckia, and Nitrosomonas at lower concentrations. Additionally, the PICRUSt functional analysis revealed the predominance of metabolism as the functional module’s primary component in both soils spiked with 0.01% and 0.1% PA. Overall, the results elucidated that PA application in soil at lower concentrations promoted soil DHA and microbial enrichment, particularly the PGPB genera, and thus have great implications for improving soil health.

scholarly journals Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Aspen T. Reese ◽  
Anne A. Madden ◽  
Marie Joossens ◽  
Guylaine Lacaze ◽  
Robert R. Dunn
Keyword(s):  
Microbial Community ◽  
Internal Transcribed Spacer ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Relative Importance ◽  
Naturally Occurring ◽  
Sourdough Bread ◽  
Bacteria And Fungi ◽  
Bidirectional Exchange

ABSTRACT Sourdough starters are naturally occurring microbial communities in which the environment, ingredients, and bakers are potential sources of microorganisms. The relative importance of these pools remains unknown. Here, bakers from two continents used a standardized recipe and ingredients to make starters that were then baked into breads. We characterized the fungi and bacteria associated with the starters, bakers’ hands, and ingredients using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing and then measured dough acidity and bread flavor. Starter communities were much less uniform than expected, and this variation manifested in the flavor of the bread. Starter communities were most similar to those found in flour but shared some species with the bakers’ skin. While humans likely contribute microorganisms to the starters, the reverse also appears to be true. This bidirectional exchange of microorganisms between starters and bakers highlights the importance of microbial diversity on bodies and in our environments as it relates to foods. IMPORTANCE Sourdough starters are complex communities of yeast and bacteria which confer characteristic flavor and texture to sourdough bread. The microbes present in starters can be sourced from ingredients or the baking environment and are typically consistent over time. Herein, we show that even when the recipe and ingredients for starter and bread are identical, different bakers around the globe produce highly diverse starters which then alter bread acidity and flavor. Much of the starter microbial community comes from bread flour, but the diversity is also associated with differences in the microbial community on the hands of bakers. These results indicate that bakers may be a source for yeast and bacteria in their breads and/or that bakers’ jobs are reflected in their skin microbiome.

scholarly journals Microbial Composition of Human Appendices from Patients following Appendectomy

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Caitriona M. Guinane ◽  
Amany Tadrous ◽  
Fiona Fouhy ◽  
C. Anthony Ryan ◽  
Eugene M. Dempsey ◽  
...  
Keyword(s):  
Human Health ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Evolutionary Development ◽  
Rrna Gene ◽  
Limited Data ◽  
Microbial Composition ◽  
Content Type ◽  
Study Results ◽  
Human Appendix

ABSTRACT The human appendix has historically been considered a vestige of evolutionary development with an unknown function. While limited data are available on the microbial composition of the appendix, it has been postulated that this organ could serve as a microbial reservoir for repopulating the gastrointestinal tract in times of necessity. We aimed to explore the microbial composition of the human appendix, using high-throughput sequencing of the 16S rRNA gene V4 region. Seven patients, 5 to 25 years of age, presenting with symptoms of acute appendicitis were included in this study. Results showed considerable diversity and interindividual variability among the microbial composition of the appendix samples. In general, however, Firmicutes was the dominant phylum, with the majority of additional sequences being assigned at various levels to Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. Despite the large diversity in the microbiota found within the appendix, however, a few major families and genera were found to comprise the majority of the sequences present. Interestingly, also, certain taxa not generally associated with the human intestine, including the oral pathogens Gemella, Parvimonas, and Fusobacterium, were identified among the appendix samples. The prevalence of genera such as Fusobacterium could also be linked to the severity of inflammation of the organ. We conclude that the human appendix contains a robust and varied microbiota distinct from the microbiotas in other niches within the human microbiome. The microbial composition of the human appendix is subject to extreme variability and comprises a diversity of biota that may play an important, as-yet-unknown role in human health. IMPORTANCE There are currently limited data available on the microbial composition of the human appendix. It has been suggested, however, that it may serve as a “safe house” for commensal bacteria that can reinoculate the gut at need. The present study is the first comprehensive view of the microbial composition of the appendix as determined by high-throughput sequencing. We have determined that the human appendix contains a wealth of microbes, including members of 15 phyla. Important information regarding the associated bacterial diversity of the appendix which will help determine the role, if any, the appendix microbiota has in human health is presented.

scholarly journals The Equine Faecal Microbiota Undergoes Step-wise Compositional Changes in Accordance With Increasing Levels of Domestication

2021 ◽  
Author(s):  
Katie Bull ◽  
Gareth Davies ◽  
Timothy Patrick Jenkins ◽  
Laura Elizabeth Peachey
Keyword(s):  
Adult Female ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Faecal Samples ◽  
High Incidence ◽  
Life Threatening ◽  
Group Variation ◽  
The Uk

Abstract BackgroundChanges to the gut microbiota are associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathology. Horses are a prime example of a species which suffers from a high incidence of (often life-threatening) GI diseases in domesticated environments. We aimed to indentify the gut microbial changes which occur due to domestication in horses by profiling the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of domestication.MethodsFaecal samples were collected from 29 adult female Exmoor ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions; thus controlling for age, gender and random effects between groups. Diet and medication were recorded and faecal samples taken to assess parasite infection. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene.ResultsDownstream biostatistical analysis indicated profound step-wise changes in global microbial community structure in the transition from Feral to Semi-Feral to Domesticated groups. A relatively high abundance of members of the phylum Proteobacteria and Tenericutes were associated with the Domesticated group; and higher levels of Methanobacteria were seen in the Feral group. The Semi-Feral group frequently had intermediate levels of these taxa; however, they also exhibited the greatest ‘within group’ variation in bacterial diversity and parasites burdens. Functional predictions revealed increased amino acid and lipid metabolism in the Domesticated group and increased energy metabolism in the Feral group; supporting a hypothesis that differences in diet was the key driver of gut microbial composition. ConclusionsIf assumed the Feral population has a more natural gut microbial phenotype, akin to that with which horses have evolved, these data can potentially be used to provide microbial signitures of balanced gut homeostasis in horses; which, in turn, will aid prevention of GI disease in domesticated horses.

scholarly journals Biliary microbiota and bile acids composition in cholelithiasis

2018 ◽  
Author(s):  
Vyacheslav A. Petrov ◽  
María A. Fernández-Peralbo ◽  
Rico Derks ◽  
Elena M. Knyazeva ◽  
Nikolay V. Merzlikin ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bile Acids ◽  
Acid Concentration ◽  
Gallstone Disease ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Taurocholic Acid ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Taxonomic Profile

AbstractBackgroundA functional interplay between BAs and microbial composition in gut is a well-documented phenomenon. In bile this phenomenon is far less studied and with this report we describe the interactions between the BAs and microbiota in this complex biological matrix.MethodologyThirty-seven gallstone disease patients of which twenty-one withOpisthorchis felineusinfection were enrolled in the study. The bile samples were obtained during laparoscopic cholecystectomy for gallstone disease operative treatment. Common bile acids composition were measured by LC-MS/MS using a column in reverse phase. For all patients gallbladder microbiota was previously analyzed with 16S rRNA gene sequencing on Illumina MiSeq platform. The associations between bile acids composition and microbiota were analysed.Principal findingsBile acids signature andO. felineusinfection status exerts influence on beta-diversity of bile microbial community. Direct correlations were found between taurocholic acid, taurochenodeoxycholic acid concentrations and alpha-diversity of bile microbiota. Taurocholic acid and taurochenodeoxycholic acid both shows positive associations with the presence of Chitinophagaceae family,MicrobacteriumandLutibacteriumgenera andPrevotella intermedia. Also direct associations were identified for taurocholic acid concentration and the presence of Actinomycetales and Bacteroidales orders,Lautropiagenus,Jeotgalicoccus psychrophilusandHaemophilus parainfluenzaeas well as for taurochenodeoxycholic acid and Acetobacteraceae family and Sphingomonas genus. There were no differences in bile acids concentrations between O.felineusinfected and non-infected patients.Conclusions/SignificanceAssociations between diversity, taxonomic profile of bile microbiota and bile acids levels were evidenced in patients with cholelithiasis. Increase of taurochenodeoxycholic acid and taurocholic acid concentration correlates with bile microbiota alpha-diversity and appearance of opportunistic pathogens. Alteration of bile acids signature could cause shifts in bile microbial community structure.

Sign in / Sign up

Export Citation Format

Share Document