Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba

AbstractThe evaluation of symbiotic microbial communities occurring in the intestinal tract of animals has received great interest in recent years. However, little is known about gut microbial communities in cetaceans, despite their relevance in the ecology of marine communities. Here, we report an investigation using 16S rRNA gene amplicon sequencing of the resident gut microbiota of the two cetacean species Stenella coeruleoalba and Tursiops truncatus by sampling intestinal mucosa from specimens retrieved stranded along the Tyrrhenian coast of Tuscany (Italy). We found an abundance of members from Clostridiaceae and Fusobacteriaceae, which in total accounted for more than 50% of reads, in agreement with gut microbiota composition of other carnivorous mammals. Probably due to the limited number of samples available, sex, preservation status and also species, did not correlate with overall differences in the microbiota. Indeed, a high similarity of the taxonomic (family-level) composition between the gut microbiota of the two species was found. However, Pedobacter spp. was found abundant in amplicon sequencing libraries from S. coeruleoalba, while clostridia were more abundant from T. truncatus samples. Our results shed some light on the gut microbiota composition of two dolphin (S. coeruleoalba and T. truncatus) species, with specimens collected in the wild. Studies with a larger number of individuals are now needed to confirm these first results and evaluate the interspecific differences in relation to sex and age.

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Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut

mBio ◽

10.1128/mbio.00687-15 ◽

2015 ◽

Vol 6 (5) ◽

Cited By ~ 50

Author(s):

Sandi Wong ◽

W. Zac Stephens ◽

Adam R. Burns ◽

Keaton Stagaman ◽

Lawrence A. David ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Dietary Fat ◽

Rrna Gene ◽

Microbiota Composition ◽

Ideal Model ◽

Surrounding Environment ◽

Animal Hosts ◽

The Relationship ◽

Gut Microbiota Composition

ABSTRACT Gut microbiota influence the development and physiology of their animal hosts, and these effects are determined in part by the composition of these microbial communities. Gut microbiota composition can be affected by introduction of microbes from the environment, changes in the gut habitat during development, and acute dietary alterations. However, little is known about the relationship between gut and environmental microbiotas or about how host development and dietary differences during development impact the assembly of gut microbiota. We sought to explore these relationships using zebrafish, an ideal model because they are constantly immersed in a defined environment and can be fed the same diet for their entire lives. We conducted a cross-sectional study in zebrafish raised on a high-fat, control, or low-fat diet and used bacterial 16S rRNA gene sequencing to survey microbial communities in the gut and external environment at different developmental ages. Gut and environmental microbiota compositions rapidly diverged following the initiation of feeding and became increasingly different as zebrafish grew under conditions of a constant diet. Different dietary fat levels were associated with distinct gut microbiota compositions at different ages. In addition to alterations in individual bacterial taxa, we identified putative assemblages of bacterial lineages that covaried in abundance as a function of age, diet, and location. These results reveal dynamic relationships between dietary fat levels and the microbial communities residing in the intestine and the surrounding environment during ontogenesis. IMPORTANCE The ability of gut microbiota to influence host health is determined in part by their composition. However, little is known about the relationship between gut and environmental microbiotas or about how ontogenetic differences in dietary fat impact gut microbiota composition. We addressed these gaps in knowledge using zebrafish, an ideal model organism because their environment can be thoroughly sampled and they can be fed the same diet for their entire lives. We found that microbial communities in the gut changed as zebrafish aged under conditions of a constant diet and became increasingly different from microbial communities in their surrounding environment. Further, we observed that the amount of fat in the diet had distinct age-specific effects on gut community assembly. These results reveal the complex relationships between microbial communities residing in the intestine and those in the surrounding environment and show that these relationships are shaped by dietary fat throughout the life of animal hosts.

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Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients

Genes ◽

10.3390/genes10100748 ◽

2019 ◽

Vol 10 (10) ◽

pp. 748 ◽

Cited By ~ 5

Author(s):

Jin-Young Lee ◽

Mohamed Mannaa ◽

Yunkyung Kim ◽

Jehun Kim ◽

Geun-Tae Kim ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gut Microbiota ◽

Gut Microbiome ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Microbiota Composition ◽

Stool Samples ◽

Gut Microbiota Composition

The aim of this study was to investigate differences between the gut microbiota composition in patients with rheumatoid arthritis (RA) and those with osteoarthritis (OA). Stool samples from nine RA patients and nine OA patients were collected, and DNA was extracted. The gut microbiome was assessed using 16S rRNA gene amplicon sequencing. The structures and differences in the gut microbiome between RA and OA were analyzed. The analysis of diversity revealed no differences in the complexity of samples. The RA group had a lower Bacteroidetes: Firmicutes ratio than did the OA group. Lactobacilli and Prevotella, particularly Prevotella copri, were more abundant in the RA than in the OA group, although these differences were not statistically significant. The relative abundance of Bacteroides and Bifidobacterium was lower in the RA group. At the species level, the abundance of certain bacterial species was significantly lower in the RA group, such as Fusicatenibacter saccharivorans, Dialister invisus, Clostridium leptum, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bacteroides faecichinchillae, Harryflintia acetispora, Bacteroides acidifaciens, and Christensenella minuta. The microbial properties of the gut differed between RA and OA patients, and the RA dysbiosis revealed results similar to those of other autoimmune diseases, suggesting that a specific gut microbiota pattern is related to autoimmunity.

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The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile

Microorganisms ◽

10.3390/microorganisms8050677 ◽

2020 ◽

Vol 8 (5) ◽

pp. 677 ◽

Cited By ~ 3

Author(s):

Monique J. T. Crobach ◽

Quinten R. Ducarmon ◽

Elisabeth M. Terveer ◽

Celine Harmanus ◽

Ingrid M. J. G. Sanders ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbiota Composition ◽

Clostridioides Difficile ◽

Bacterial Microbiota ◽

Differential Abundance Analysis ◽

Gut Microbiota Composition ◽

Eubacterium Hallii

Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p < 0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients’ gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.

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Plasma Metabolites Related to Peripheral and Hepatic Insulin Sensitivity Are Not Directly Linked to Gut Microbiota Composition

Nutrients ◽

10.3390/nu12082308 ◽

2020 ◽

Vol 12 (8) ◽

pp. 2308

Author(s):

Annefleur M. Koopen ◽

Nicolien C. de Clercq ◽

Moritz V. Warmbrunn ◽

Hilde Herrema ◽

Mark Davids ◽

...

Keyword(s):

Insulin Sensitivity ◽

Gut Microbiota ◽

Prediction Models ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Plasma Metabolites ◽

Rrna Gene ◽

Microbiota Composition ◽

Cross Sectional ◽

Gut Microbiota Composition

Plasma metabolites affect a range of metabolic functions in humans, including insulin sensitivity (IS). A subset of these plasma metabolites is modified by the gut microbiota. To identify potential microbial–metabolite pathways involved in IS, we investigated the link between plasma metabolites, gut microbiota composition, and IS, using the gold-standard for peripheral and hepatic IS measurement in a group of participants with metabolic syndrome (MetSyn). In a cross-sectional study with 115 MetSyn participants, fasting plasma samples were collected for untargeted metabolomics analysis and fecal samples for 16S rRNA gene amplicon sequencing. A two-step hyperinsulinemic euglycemic clamp was performed to assess peripheral and hepatic IS. Collected data were integrated and potential interdependence between metabolites, gut microbiota, and IS was analyzed using machine learning prediction models. Plasma metabolites explained 13.2% and 16.7% of variance in peripheral and hepatic IS, respectively. Fecal microbiota composition explained 4.2% of variance in peripheral IS and was not related to hepatic IS. Although metabolites could partially explain the variances in IS, the top metabolites related to peripheral and hepatic IS did not significantly correlate with gut microbiota composition (both on taxonomical level and alpha-diversity). However, all plasma metabolites could explain 18.5% of the variance in microbial alpha-diversity (Shannon); the top 20 metabolites could even explain 44.5% of gut microbial alpha-diversity. In conclusion, plasma metabolites could partially explain the variance in peripheral and hepatic IS; however, these metabolites were not directly linked to the gut microbiota composition, underscoring the intricate relation between plasma metabolites, the gut microbiota, and IS in MetSyn

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The effect of toxic pyridine-alkaloid secondary metabolites on the sunbird gut microbiome

npj Biofilms and Microbiomes ◽

10.1038/s41522-020-00161-9 ◽

2020 ◽

Vol 6 (1) ◽

Author(s):

Mohanraj Gunasekaran ◽

Maya Lalzar ◽

Yehonatan Sharaby ◽

Ido Izhaki ◽

Malka Halpern

Keyword(s):

Secondary Metabolites ◽

Gut Microbiota ◽

Gut Microbiome ◽

Amplicon Sequencing ◽

Control Group ◽

Rrna Gene ◽

Microbiota Composition ◽

Degrading Bacteria ◽

And Control ◽

Gut Microbiota Composition

AbstractSunbirds feed on tobacco tree nectar which contains toxic nicotine and anabasine secondary metabolites. Our aim was to understand the effect of nicotine and anabasine on the gut microbiota composition of sunbirds. Sixteen captive sunbirds were randomly assigned to two diets: artificial nectar either with (treatment) or without (control) added nicotine and anabasine. Excreta were collected at 0, 2, 4 and 7 weeks of treatment and samples were processed for bacterial culture and high-throughput amplicon sequencing of the 16S rRNA gene. The gut microbiome diversity of the treated and control birds changed differently along the seven-week experiment. While the diversity decreased in the control group along the first three samplings (0, 2 and 4 weeks), it increased in the treatment group. The microbiota composition analyses demonstrated that a diet with nicotine and anabasine, significantly changed the birds’ gut microbiota composition compared to the control birds. The abundance of nicotine- and anabasine- degrading bacteria in the excreta of the treated birds, was significantly higher after four and seven weeks compared to the control group. Furthermore, analysis of culturable isolates, including Lactococcus, showed that sunbirds’ gut-associated bacteria were capable of degrading nicotine and anabasine, consistent with their hypothesised role as detoxifying and nutritional symbionts.

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Implications of Tributyrin on Gut Microbiota Shifts Related to Performances of Weaning Piglets

Microorganisms ◽

10.3390/microorganisms9030584 ◽

2021 ◽

Vol 9 (3) ◽

pp. 584

Author(s):

Francesco Miragoli ◽

Vania Patrone ◽

Aldo Prandini ◽

Samantha Sigolo ◽

Matteo Dell’Anno ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Average Daily Gain ◽

Basal Diet ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Microbiota Composition ◽

Growth Promoters ◽

Weaning Piglets ◽

Gut Microbiota Composition

Alternatives to antibiotic treatments are required owing to the ban on the use of these drugs as growth promoters in food animal production. Tributyrin appears to play a role in improving growth performance in pigs, albeit with varying degrees of effectiveness. So far, very little is known about its effects on gut microbiota composition. In this study, we investigated the gut microbiota changes of piglets receiving, at weaning, 0.2% tributyrin added to their basal diet. Microbiota composition was assessed through 16S-rRNA gene sequencing on stools collected from tributyrin and control groups. The functional profiles of microbial communities were predicted from amplicon abundance data. A comparison between dietary groups revealed that tributyrin strongly modulated gut microbiota composition in piglets, increasing the relative abundance of a number of bacterial genera such as Oscillospira, Oscillibacter, Mucispirillum and Butyrivibrio. These genera were positively correlated to animal average daily gain (ADG) and/or body weight (BW). Based on the function profile prediction, the gut microbiome of the tributyrin group possessed an enhanced potential for energy metabolism and a reduced potential for carbohydrate metabolism. In conclusion, our results indicated that tributyrin can promote changes to gut microbial communities, which could contribute to improving animal performance after weaning.

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The microbial community of the gut differs between piglets fed sow milk, milk replacer or bovine colostrum

British Journal Of Nutrition ◽

10.1017/s0007114517000216 ◽

2017 ◽

Vol 117 (7) ◽

pp. 964-978 ◽

Cited By ~ 8

Author(s):

Ann-Sofie R. Poulsen ◽

Nadieh de Jonge ◽

Sugiharto Sugiharto ◽

Jeppe L. Nielsen ◽

Charlotte Lauridsen ◽

...

Keyword(s):

Gut Microbiota ◽

Amplicon Sequencing ◽

Bovine Colostrum ◽

Milk Replacer ◽

Rrna Gene ◽

Bacterial Dna ◽

Faecal Samples ◽

Milk Replacers ◽

The 16S Rrna Gene ◽

Gut Microbiota Composition

AbstractThe aim of this study was to characterise the gut microbiota composition of piglets fed bovine colostrum (BC), milk replacer (MR) or sow milk (SM) in the post-weaning period. Piglets (n36), 23-d old, were randomly allocated to the three diets. Faecal samples were collected at 23, 25, 27 and 30 d of age. Digesta from the stomach, ileum, caecum and mid-colon was collected at 30 d of age. Bacterial DNA from all samples was subjected to amplicon sequencing of the 16S rRNA gene. Bacterial enumerations by culture and SCFA analysis were conducted as well. BC-piglets had the highest abundance ofLactococcusin the stomach (P<0·0001) and ileal (P<0·0001) digesta, whereas SM-piglets had the highest abundance ofLactobacillusin the stomach digesta (P<0·0001). MR-piglets had a high abundance of Enterobacteriaceae in the ileal digesta (P<0·0001) and a higher number of haemolytic bacteria in ileal (P=0·0002) and mid-colon (P=0·001) digesta than SM-piglets. BC-piglets showed the highest colonic concentration of iso-butyric and iso-valeric acid (P=0·02). Sequencing and culture showed that MR-piglets were colonised by a higher number of Enterobacteriaceae, whereas the gut microbiota of BC-piglets was characterised by a change in lactic acid bacteria genera when compared with SM-piglets. We conclude that especially the ileal microbiota of BC-piglets had a closer resemblance to that of SM-piglets in regard to the abundance of potential enteric pathogens than did MR-piglets. The results indicate that BC may be a useful substitute for regular milk replacers, and as a feeding supplement in the immediate post-weaning period.

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Colonisation potential of plantaricin-producing Lactobacillus plantarum SF9C andS-layer-carrying Lactobacillus brevis SF9B among gut microbiota

10.21203/rs.2.23400/v2 ◽

2020 ◽

Author(s):

Katarina Butorac ◽

Martina Banic ◽

Jasna Novak ◽

Andreja Leboš Pavunc ◽

Ksenija Uroic ◽

...

Keyword(s):

Gut Microbiota ◽

Lactobacillus Plantarum ◽

Lactobacillus Brevis ◽

Illumina Miseq ◽

Rrna Gene ◽

Microbiota Composition ◽

Combined Application ◽

Probiotic Potential ◽

Gut Microbiota Composition

Abstract Background: The influence of an S-layer-carrying strain Lactobacillus brevis SF9B and a plantaricin-producing strain Lactobacillus plantarum SF9C on the gut microbiota composition was evaluated in the rats. Considering the probiotic potential of Lb. brevis SF9B, this study aimed to examine the antibacterial activity of Lb. plantarum SF9C and potential for their in vivo colonisation, which could be the basis for the investigation of their synergistic functionality. Results: A plantaricin-encoding cluster was identified in Lb. plantarum SF9C, a strain which efficiently inhibited the growth of Listeria monocytogenes ATCC®19111™ and Staphylococcus aureus 3048. Contrary to the plantaricin-producing SF9C strain, the S-layer-carrying SF9B strain excluded Escherichia coli 3014 and Salmonella enterica serovar Typhimurium FP1 from adhesion to Caco-2 cells. Finally, DGGE analysis of the V2-V3 region of the 16S rRNA gene confirmed the transit of two selected lactobacilli through the gastrointestinal tract (GIT). Microbiome profiling via the Illumina MiSeq platform revealed the prevalence of Lactobacillus spp. in the gut microbiota of rats suggesting their colonisation potential in GIT.Conclusion: The combined application of Lb. plantarum SF9C and Lb. brevis SF9B could influence the intestinal microbiota composition, which is reflected through the increased abundance of Lactobacillus genus, but also through altered abundances of other bacterial genera, either in the model of healthy or aberrant microbiota of rats. The obtained results contributed to the functional aspects of SF9C and SF9B strains which could be incorporated in the probiotic-containing functional foods and therefore have a beneficial influence on the gut microbiota composition.

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Changes in the gut microbiota of morbidly obese patients after laparoscopic sleeve gastrectomy

Future Microbiology ◽

10.2217/fmb-2021-0043 ◽

2021 ◽

Author(s):

Alev Kural ◽

Imran Khan ◽

Hakan Seyit ◽

Tuba R Caglar ◽

Pınar Toklu ◽

...

Keyword(s):

Sleeve Gastrectomy ◽

Gut Microbiota ◽

Laparoscopic Sleeve Gastrectomy ◽

Amplicon Sequencing ◽

Morbidly Obese ◽

Microbiota Composition ◽

16S Amplicon Sequencing ◽

Before And After ◽

Stool Samples ◽

Gut Microbiota Composition

Aims: Permanent treatment of morbid obesity with medication or diet is nearly impossible. Laparoscopic sleeve gastrectomy (LSG) is becoming a widely accepted treatment option. This study profiled and compared gut microbiota composition before and after LSG. Methods & results: A total of 54 stool samples were collected from 27 morbidly obese individuals before and after LSG. The gut microbiota was profiled with 16S amplicon sequencing. After LSG, patients demonstrated a significant decrease (p < 0.001) in BMI and an increase in bacterial diversity. An increased Firmicutes/Bacteroidetes ratio was also noticed after LSG. The families Prevotellaceae and Veillonellaceae predominated in preoperative samples but were markedly lowered after LSG. A marked increase in Akkermansia, Alistipes, Streptococcus, Ruminococcus and Parabacteroides was observed after LSG. Conclusion: In addition to lowering BMI, LSG remodeled gut microbiota composition.

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IgA-deficient humans exhibit gut microbiota dysbiosis despite secretion of compensatory IgM

Scientific Reports ◽

10.1038/s41598-019-49923-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 24

Author(s):

Jason R. Catanzaro ◽

Juliet D. Strauss ◽

Agata Bielecka ◽

Anthony F. Porto ◽

Francis M. Lobo ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Iga Deficiency ◽

Secretory Iga ◽

Rrna Gene ◽

Healthy Controls ◽

Microbiota Composition ◽

Antibody Isotype ◽

Selective Iga Deficiency ◽

Gut Microbiota Composition

Abstract Immunoglobulin A is the dominant antibody isotype found in mucosal secretions and enforces host-microbiota symbiosis in mice, yet selective IgA-deficiency (sIgAd) in humans is often described as asymptomatic. Here, we determined the effects of IgA deficiency on human gut microbiota composition and evaluated the possibility that mucosal secretion of IgM can compensate for a lack of secretory IgA. We used 16S rRNA gene sequencing and bacterial cell sorting to evaluate gut microbiota composition and taxa-specific antibody coating of the gut microbiota in 15 sIgAd subjects and matched controls. Despite the secretion of compensatory IgM into the gut lumen, sIgAd subjects displayed an altered gut microbiota composition as compared to healthy controls. These alterations were characterized by a trend towards decreased overall microbial diversity as well as significant shifts in the relative abundances of specific microbial taxa. While secretory IgA in healthy controls targeted a defined subset of the microbiota via high-level coating, compensatory IgM in sIgAd subjects showed less specificity than IgA and bound a broader subset of the microbiota. We conclude that IgA plays a critical and non-redundant role in controlling gut microbiota composition in humans and that secretory IgA has evolved to maintain a diverse and stable gut microbial community.

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