Covariation of the gut microbiome with diet in Aves

Abstract Background:Research over the past few decades has revealed a vital role for the gut microbiome in the health of various animals including birds. Multiple factors can influence the gut microbiome. Opportunistic feeding and multiple other environment factors can influence the results, and bias the conclusions, when wild animals are used to study the influence of phylogeny and diet on their gut microbiomes. Therefore, to study this question in this study, we collected fecal samples from 43 species of Aves at one time to avoid influences such as geography, weather, and season. Results:Approaches based on both 16S rRNA gene sequencing (135 samples) and whole metagenome shotgun sequencing (17 samples) were used. Our data show that diets containing native starch will increase the abundance of Lactobacillus in gut microbiome, while those containing plant-derived fiber will mainly enrich the levels of Clostridium. Greater numbers of Fusobacteria and Proteobacteria are detected in carnivorous birds, while in birds fed a commercial corn-soybean basal diet, a stronger inner-connected microbial community containing Clostridia and Bacteroidia was enriched. Furthermore, a microbial functional analysis based on the metagenomic sequences showed that the function of microbes was adapted to different food types to achieve the most beneficial state for the hosts. Conclusions:The covariation of diet and gut microbiome identified in our study demonstrates modulation of the gut microbiome by dietary diversity and expands our knowledge of diet-microbiome-host interactions in birds.

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Gut Microbiome of Two Different Honeybee Workers Subspecies In Saudi Arabia.

Biosciences Biotechnology Research Asia ◽

10.13005/bbra/2870 ◽

2021 ◽

Vol 17 (4) ◽

pp. 659-671

Author(s):

Marfat Alatawy ◽

Sanaa G. Al-Attas ◽

Ahmad I. Assagaf ◽

Rashad R. Al-Hindi ◽

Khalid M. Alghamdi ◽

...

Keyword(s):

Saudi Arabia ◽

16S Rrna ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Vital Role ◽

Rrna Gene ◽

Microbiome Diversity ◽

Rrna Gene Sequencing ◽

Honeybee Subspecies ◽

Different Origins

Honeybees play a vital role in the world’s food supply by acting as essential pollinators in the agricultural fields. Interestingly, more than one third of the world’s essential crops are honeybee’s dependant. The adult honeybeeworkers harbour a simple specific bacterial spectrum in their guts with vital role in bees’ health. Gut microbial diversity of adult honeybee workerswasstudied through targeting the V3 and V4 regions of the 16S rRNA geneviaIllumina MiSeq. The study identified four phyla of the gut microbiomesinadult workersof the two-honeybee subspecies A.m. jemeniticaandA.m. carnica. The most abundant phylum in microbiome of A.m. jemeniticawasFirmicutes (48%), while Protobacteria and Actinobacteriaphylawere less abundantat figures of31% and 10%, respectively. In microbiome of A.m. carnica,Firmicutes (57%) was also the most dominant phylum, while Protobacteria and Actinobacteria had lower prevalence at figures of 31% and 10%, respectively. At genus level, adult honeybee workers harboured a number ofLactobacillus spp.in their guts with relative abundance of 80% in A.m. jemeniticaworkers compared to52%forA.m. carnicaworkers.Up toour knowledge, this is the first study of its kind on gut microbiome diversity inhoneybee workersof different origins conducted in Saudi Arabia using high-throughput 16S rRNA gene sequencing technology. The results indicatedthat the variability inmonophyletic origin of host of honeybee workers affectedgut microbiota composition.

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

Scientific Reports ◽

10.1038/s41598-020-80557-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Esteban Góngora ◽

Kyle H. Elliott ◽

Lyle Whyte

Keyword(s):

Gut Microbiome ◽

Sulfur Isotopes ◽

Trophic Position ◽

Isotope Analysis ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Uria Lomvia ◽

Fecal Microbiome ◽

Prey Specialization ◽

Rrna Gene Sequencing

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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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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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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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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Association between premature ovarian insufficiency and gut microbiota

BMC Pregnancy and Childbirth ◽

10.1186/s12884-021-03855-w ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jiaman Wu ◽

Yuanyuan Zhuo ◽

Yulei Liu ◽

Yan Chen ◽

Yan Ning ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiome ◽

Ovarian Function ◽

16S Rrna Gene Sequencing ◽

Serum Levels ◽

Premature Ovarian Insufficiency ◽

Rrna Gene ◽

Ovarian Insufficiency ◽

Healthy Women ◽

Rrna Gene Sequencing

Abstract Background Premature ovarian insufficiency (POI) is characterized by impairment of ovarian function on a continuum before the age of 40 years. POI is affected by multiple factors. Considering new insights from recent gut microbiome studies, this study aimed to investigate the relationship between gut microbial community structure and POI. Methods Subjects were recruited at the Shenzhen Maternity & Child Healthcare Hospital. Fecal microbial community profiles of healthy women (n = 18), women with POI (n = 35) were analyzed using 16S rRNA gene sequencing based on Illumina NovaSeq platform. Results Compared to the controls, the serum levels of FSH, LH, T and FSH/LH ratio significantly increased in women with POI, whereas E2 and AMH decreased significantly. Higher weighted UniFrac value was observed in POI women compared with healthy women. Phylum Firmicutes, genera Bulleidia and Faecalibacterium were more abundant in healthy women, while phylum Bacteroidetes, genera Butyricimonas, Dorea, Lachnobacterium and Sutterella enriched significantly in women with POI. Moreover, these alterations of the gut microbiome in women with POI were closely related to FSH, LH, E2, AMH level and FSH/LH ratio. Conclusions Women with POI had altered microbial profiles in their gut microbiome, which were associated with serum hormones levels. These results will shed a new light on the pathogenesis and treatment for POI.

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