Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

AbstractThe role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

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Fecal microbiota and diet compositions of muskox female adults and calves

10.22541/au.164171940.09418250/v1 ◽

2022 ◽

Author(s):

Ji-Yeon Cheon ◽

Hyunjoon Cho ◽

Mincheol Kim ◽

Hyun Je Park ◽

Tae-Yoon Park ◽

...

Keyword(s):

Gut Microbiome ◽

Isotope Analysis ◽

16S Rrna Gene Sequencing ◽

High Arctic ◽

Fecal Microbiota ◽

Rrna Gene ◽

Large Herbivore ◽

Rrna Gene Sequencing ◽

The One ◽

Salix Glauca

Gut microbiome is vertically transmitted by maternal lactation at birth in mammals. In this study, we investigated the gut microbiome and diet compositions of muskox, a large herbivore in the high Arctic. From muskox feces in Ella Island, East Greenland, we compared the microbiota composition using bacterial 16S rRNA gene sequencing and the dietary compositions of six female adults and four calves have been compared. Firmicutes was the most abundant bacterial phylum in both adults and calves, comprising 94.36% and 94.03%, respectively. There were significant differences in the relative abundance of two Firmicutes families: the adults were mainly dominated by Ruminococcaceae (73.90%), while the calves were dominated by both Ruminococcaceae (56.25%) and Lachnospiraceae (24.00%). Stable isotope analysis on the feces and eight referential plant samples in the study area showed that both adults and calves had similar ranges of 13C and 15N, possibly derived from the dominant diet plants of Empetrum nigrum and Salix glauca. Despite the similar diets, the different gut microbiome compositions in muskox adults and calves indicate that the gut microbiome of the calves may not be fully colonized yet as much as the one of the adults.

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Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

PLoS ONE ◽

10.1371/journal.pone.0212474 ◽

2019 ◽

Vol 14 (2) ◽

pp. e0212474 ◽

Cited By ~ 1

Author(s):

Daniel E. Almonacid ◽

Laurens Kraal ◽

Francisco J. Ossandon ◽

Yelena V. Budovskaya ◽

Juan Pablo Cardenas ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gut Microbiome ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Reference Ranges ◽

Human Gut ◽

Human Gut Microbiome ◽

Rrna Gene Sequencing

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Long-Term Recovery of the Fecal Microbiome and Metabolome of Dogs with Steroid-Responsive Enteropathy

Animals ◽

10.3390/ani11092498 ◽

2021 ◽

Vol 11 (9) ◽

pp. 2498

Author(s):

Rachel Pilla ◽

Blake C Guard ◽

Amanda B Blake ◽

Mark Ackermann ◽

Craig Webb ◽

...

Keyword(s):

16S Rrna ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Elimination Diet ◽

Rrna Gene ◽

Fecal Microbiome ◽

Rrna Gene Sequencing ◽

One Year ◽

Long Term Impact

The long-term impact of treatment of dogs with steroid-responsive enteropathy (SRE) on the fecal microbiome and metabolome has not been investigated. Therefore, this study aimed to evaluate the fecal microbiome and metabolome of dogs with SRE before, during, and following treatment with standard immunosuppressive therapy and an elimination diet. We retrospectively selected samples from 9 dogs with SRE enrolled in a previous clinical trial, which received treatment for 8 weeks, and had achieved remission as indicated by the post-treatment clinical scores. Long-term (1 year) samples were obtained from a subset (5/9) of dogs. Samples from 13 healthy dogs were included as controls (HC). We evaluated the microbiome using 16S rRNA sequencing and qPCR. To evaluate the recovery of gut function, we measured fecal metabolites using an untargeted approach. While improvement was observed for some bacterial taxa after 8 weeks of treatment, several bacterial taxa remained significantly different from HC. Seventy-five metabolites were altered in dogs with SRE, including increased fecal amino acids and vitamins, suggesting malabsorption as a component of SRE. One year after treatment, however, all bacterial species were evaluated by qPCR and 16S rRNA gene sequencing, and all but thirteen metabolites were no longer different from healthy controls.

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The Effect of Xuebijing on the Gut Microbiota and Metabolic of Heat 1 Stroke Rat 2

10.21203/rs.3.rs-142370/v1 ◽

2021 ◽

Author(s):

Qiang wen ◽

Xuan He ◽

Yu Shao ◽

Lun Peng ◽

Li Zhao ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gut Microbiome ◽

Heat Stroke ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Control Group ◽

Rrna Gene ◽

Metabolism Pathway ◽

Rrna Gene Sequencing

Abstract The goal of the present study was to evaluate the fecal microbiome and serum metabolites in 16 Xuebijing (XBJ)-injected rats after heat stroke using 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics. Eighteen rats were divided into the control group (CON), heat stroke group (HS), and XBJ group. The 16S rRNA gene sequencing results revealed that the abundance of Bacteroidetes was overrepresented in the XBJ group compared to the HS group, while Actinobacteria was underrepresented. Metabolomic profiling showed that the pyrimidine metabolism pathway, pentose phosphate pathway, and glycerophospholipid metabolism pathway were upregulated in the XBJ group compared to the HS group. Taken together, these results demonstrated that heat stroke not only altered the gut microbiome community structure of rats but also greatly affected metabolic functions, leading to gut microbiome toxicity.

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Dietary sphinganine is selectively assimilated by members of the gut microbiome

10.1101/2020.06.08.140665 ◽

2020 ◽

Author(s):

Min-Ting Lee ◽

Henry H. Le ◽

Elizabeth L. Johnson

Keyword(s):

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Dietary Lipids ◽

Rrna Gene ◽

Bioactive Components ◽

Microbiome Composition ◽

Metabolic Products ◽

Comparative Metabolomics ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

AbstractFunctions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remain largely unknown. A class of lipids known as sphingolipids are bioactive components of most foods and are produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we use a click-chemistry based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne – SAA) into the gut microbial community (Click). Identification of microbe and SAA-specific metabolic products was achieved by fluorescence-based sorting of SAA containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together this approach, Click-Sort-Seq-Spec (ClickSSS), revealed that SAA-assimilation was nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice showed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activity via Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. Therefore, ClickSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

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Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines

Vaccines ◽

10.3390/vaccines9111356 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1356

Author(s):

Michele Tomasi ◽

Mattia Dalsass ◽

Francesco Beghini ◽

Ilaria Zanella ◽

Elena Caproni ◽

...

Keyword(s):

Gut Microbiome ◽

Cancer Vaccines ◽

Molecular Mimicry ◽

Large Body ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Shotgun Metagenomics ◽

Cancer Immunity ◽

Rrna Gene Sequencing

A large body of data both in animals and humans demonstrates that the gut microbiome plays a fundamental role in cancer immunity and in determining the efficacy of cancer immunotherapy. In this work, we have investigated whether and to what extent the gut microbiome can influence the antitumor activity of neo-epitope-based cancer vaccines in a BALB/c-CT26 cancer mouse model. Similarly to that observed in the C57BL/6-B16 model, Bifidobacterium administration per se has a beneficial effect on CT26 tumor inhibition. Furthermore, the combination of Bifidobacterium administration and vaccination resulted in a protection which was superior to vaccination alone and to Bifidobacterium administration alone, and correlated with an increase in the frequency of vaccine-specific T cells. The gut microbiome analysis by 16S rRNA gene sequencing and shotgun metagenomics showed that tumor challenge rapidly altered the microbiome population, with Muribaculaceae being enriched and Lachnospiraceae being reduced. Over time, the population of Muribaculaceae progressively reduced while the Lachnospiraceae population increased—a trend that appeared to be retarded by the oral administration of Bifidobacterium. Interestingly, in some Bacteroidales, Prevotella and Muribaculacee species we identified sequences highly homologous to immunogenic neo-epitopes of CT26 cells, supporting the possible role of “molecular mimicry” in anticancer immunity. Our data strengthen the importance of the microbiome in cancer immunity and suggests a microbiome-based strategy to potentiate neo-epitope-based cancer vaccines.

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Molecular and Microbial Signatures Predictive of Prebiotic Action of Neoagarotetraose in a Dextran Sulfate Sodium-Induced Murine Colitis Model

Microorganisms ◽

10.3390/microorganisms8070995 ◽

2020 ◽

Vol 8 (7) ◽

pp. 995

Author(s):

Fang Liu ◽

Jianan Liu ◽

Thomas T.Y. Wang ◽

Zhen Liu ◽

Changhu Xue ◽

...

Keyword(s):

Gut Microbiome ◽

Dextran Sulfate ◽

Dextran Sulfate Sodium ◽

Intestinal Inflammation ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Murine Colitis ◽

Bioactive Properties ◽

Rrna Gene Sequencing ◽

Colitis Model

Neoagarotetraose (NT), a hydrolytic product of agar by β-agarase, is known to possess bioactive properties. However, the mechanisms via which NT alleviates intestinal inflammation remain unknown. In this study, a dextran sulfate sodium (DSS)-induced murine model was developed to evaluate the effect of NT on gut microbiome and microbial metabolism using 16S rRNA gene sequencing and untargeted metabolomics. Our data demonstrate that NT ingestion improved gut integrity and inflammation scores. NT reversed the abundance of Proteobacteria from an elevated level induced by DSS and significantly increased the abundance of Verrucomicrobia. Further, NT significantly increased the abundance of Akkermansia and Lactobacillus and concomitantly decreased that of Sutterella, which were among the important features identified by random forests analysis contributing to classification accuracy for NT supplementation. A microbial signature consisting of Adlercreutzia (denominator) and Turicibacter (numerator) predicted the NT supplementation status. Moreover, NT significantly modulated multiple gut metabolites, particularly those related to histidine, polyamine and tocopherol metabolism. Together, our findings provided novel insights into the mechanisms by which NT modulated the gut microbiome and metabolome and should facilitate the development of NT as a potent prebiotic for colitis management.

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Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing

Journal of Applied Genetics ◽

10.1007/s13353-020-00575-3 ◽

2020 ◽

Vol 61 (4) ◽

pp. 593-605

Author(s):

Filippo Cendron ◽

Giovanni Niero ◽

Gabriele Carlino ◽

Mauro Penasa ◽

Martino Cassandro

Keyword(s):

16S Rrna ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Fecal Bacteria ◽

Fecal Microbiome ◽

Alpha And Beta Diversity ◽

Microbiome Composition ◽

Lactating Cows ◽

Holstein Friesian ◽

Rrna Gene Sequencing

AbstractThe aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.

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Digestive gland microbiome of Pleurobema cordatum: mesocosms induce dysbiosis

Journal of Molluscan Studies ◽

10.1093/mollus/eyaa024 ◽

2020 ◽

Vol 86 (4) ◽

pp. 280-289

Author(s):

Alison K Aceves ◽

Paul D Johnson ◽

Carla L Atkinson ◽

Brian C van Ee ◽

Stephen A Bullard ◽

...

Keyword(s):

Digestive Gland ◽

Gut Microbiome ◽

Bacterial Communities ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Artificial Rearing ◽

Tennessee River ◽

Wasting Syndrome ◽

Water And Sediment ◽

Rrna Gene Sequencing

ABSTRACT Herein, we characterized the digestive gland (‘gut’) bacterial community (microbiome) of the Ohio pigtoe, Pleurobema cordatum (Rafinesque, 1820), using 16S rRNA gene sequencing. Two populations were compared: wild P. cordatum (n = 5) from the Tennessee River and P. cordatum (n = 9) relocated to artificial mesocosms and exposed to various thermal regimes for 2 weeks. We also characterized the bacterial communities from the habitat (water and sediment) of these wild and mesocosm-held populations. The gut microbiome of wild P. cordatum was dominated by members of the bacterial phylum Tenericutes (72%). By contrast, the gut microbiome of mesocosm-held P. cordatum was dominated by members of the bacterial phylum Proteobacteria (64%). We found no temperature-associated difference in the gut microbiome of mesocosm-held P. cordatum. The bacterial communities of water and sediment from the Tennessee River were diverse and distinct from those of the studied mussels. By contrast, the bacterial communities of water and sediment in the mesocosms were dominated by Proteobacteria. These results suggest that when the studied mussels were moved into artificial rearing environments, their gut microbiome shifted to reflect that of their habitat (i.e. an increase in Proteobacteria). Moreover, the abundance of Tenericutes (also previously reported in other unionids) was reduced from 72% in wild mussels to 3% in mesocosm-held mussels. As a result, we think that mesocosm-held P. cordatum became dysbiotic, which could explain the observed wasting syndrome and associated trickling mortalities in captive P. cordatum.

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Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

The Journal of Lipid Research ◽

10.1194/jlr.ra120000950 ◽

2020 ◽

pp. jlr.RA120000950 ◽

Cited By ~ 1

Author(s):

Min-Ting Lee ◽

Henry H Le ◽

Elizabeth L Johnson

Keyword(s):

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Dietary Lipids ◽

Rrna Gene ◽

Microbiome Composition ◽

Bioorthogonal Labeling ◽

Comparative Metabolomics ◽

Metabolic Activities ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.

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