Animal Microbiome

The gut microbiota (GM) has proven to be essential for both physical health and mental wellbeing, yet the forces that ultimately shape its composition remain opaque. One critical force known to affect the GM is the social environment. Prior work in humans and free-ranging non-human primates has shown that cohabitation and frequent social interaction can lead to changes in GM composition. However, it is difficult to assess the direction of causation in these studies, and interpretations are complicated by the influence of uncontrolled but correlated factors, such as shared diet.

Colleen S Pearce

Danielle Bukovsky

Katya Douchant

Abhay Katoch

Jill Greenlaw

Daniel J Gale

Joseph Y Nashed

Don Brien

Valerie A Kuhlmeier

Mark A Sabbagh

Gunnar Blohm

Fernanda G De Felice

Martin Pare

Douglas J Cook

Stephen H Scott

Douglas P Munoz

Calvin P Sjaarda

Anita Tusche

Prameet M Sheth

Andrew Winterborn

Susan Boehnke

Jason P Gallivan

Changes in social environment impact primate gut microbiota composition

社会环境变化对灵长类肠道微生物群组成的影响

Corals are the foundational species of coral reefs and coralligenous ecosystems. Their success has been linked to symbioses with microorganisms, and a coral host and its symbionts are therefore considered a single entity, called the holobiont. This suggests that there may be evolutionary links between corals and their microbiomes. While there is evidence of phylosymbiosis in scleractinian hexacorals, little is known about the holobionts of Alcyonacean octocorals. 16S rRNA gene amplicon sequencing revealed differences in the diversity and composition of bacterial communities associated with octocorals collected from the mesophotic zones of the Mediterranean and Red Seas. The low diversity and consistent dominance of Endozoicomonadaceae and/or Spirochaetaceae in the bacterial communities of Mediterranean octocorals suggest that these corals may have a shared evolutionary history with their microbiota. Phylosymbiotic signals were indeed detected and cophylogeny in associations between several bacterial strains, particularly those belonging to Endozoicomonadaceae or Spirochaetaceae, and coral species were identified. Conversely, phylosymbiotic patterns were not evident in Red Sea octocorals, likely due to the high bacterial taxonomic diversity in their microbiota, but cophylogeny in associations between certain coral and bacterial species was observed. Noteworthy were the associations with Endozoicomonadaceae, suggesting a plausible evolutionary link that warrants further investigations to uncover potential underlying patterns. Overall, our findings emphasize the importance of Endozoicomonadaceae and Spirochaetaceae in coral symbiosis and the significance of exploring host-microbiome interactions in mesophotic ecosystems for a comprehensive understanding of coral-microbiome evolutionary history.

C. Prioux

C. Ferrier-Pages

J. Deter

R. Tignat-Perrier

A. Guilbert

L. Ballesta

D. Allemand

J. A. J. M. van de Water

Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea

地中海和红海八放珊瑚共生体中系统共生与协同进化的发生机制探究

Changes in diet causing ecological stress pose a significant challenge to animal survival. In response, the gut microbiota, a crucial part of the host's digestive system, exhibits patterns of change reflective of alterations in the host's food component. The impact of temporal dietary shifts on gut microbiota has been elucidated through multidimensional modeling of both food component and macronutrient intake. However, the broad distribution of wild generalist and the intricate complexity of their food component hinder our capacity to ascertain the degree to which their gut microbiota assist in adapting to spatial dietary variations. We examined variation in patterns of the gut microbial community according to changes in diet and in a colobine monkey with a regional variable diet, the golden snub-nosed monkey (Rhinopithecus roxellana). Specifically, we analyse the interactions between variation in food component, macronutrient intake and the gut microbial community. We compared monkeys from four populations by quantifying food component and macronutrient intake, and by sequencing 16S rRNA and the microbial macro-genomes from the faecal samples of 44 individuals. We found significant differences in the diets and gut microbial compositions, in nutrient space and macronutrient intake among some populations. Variations in gut microbiota composition across distinct populations mirror the disparities in macronutrient intake, with a notable emphasis on carbohydrate. Geographical differences in the diet among of golden snub-nosed monkey populations will result in macronutrient intake variation, with corresponding differences in macronutrient intake driving regional differences in the compositions and abundances of gut microbiota. Importantly, the gut microbiota associated with core digestive functions does not vary, with the non-core gut microbiota fluctuating in response to variation in macronutrient intake. This characteristic may enable species heavily reliant on gut microbiota for digestion to adapt to diet changes. Our results further the understanding of the roles gut microbiota play in the formation of host dietary niches.

Yuhang Li

Yujie Yan

Haojie Wu

Yiyi Men

Yi Yang

Hengguang Fu

Derek Dunn

Xiaowei Wang

Genggeng Gao

Peng Zhang

Guixin Dong

Liyuan Hao

Jia Jia

Baoguo Li

Songtao Guo

The role of gut microbiota in a generalist, golden snub-nosed monkey, adaptation to geographical diet change

通用型金丝猴肠道微生物在适应地理饮食变化中的作用

Gut microbes are important to the health and fitness of many animals. Many factors have been shown to affect gut microbial communities including diet, lifestyle, and age. Most animals have very complex physiologies, lifestyles, and microbiomes, making it virtually impossible to disentangle what factors have the largest impact on microbiota composition. Honeybees are an excellent model to study host-microbe interactions due to their relatively simple gut microbiota, experimental tractability, and eusociality. Worker honey bees have distinct gut microbiota from their queen mothers despite being close genetic relatives and living in the same environment. Queens and workers differ in numerous ways including development, physiology, pheromone production, diet, and behavior. In the prolonged absence of a queen or Queen Mandibular Pheromones (QMP), some but not all workers will develop ovaries and become "queen-like". Using this inducible developmental change, we aimed to determine if diet and/or reproductive development impacts the gut microbiota of honey bee workers. Microbiota-depleted newly emerged workers were inoculated with a mixture of queen and worker gut homogenates and reared under four conditions varying in diet and pheromone exposure. Three weeks post-emergence, workers were evaluated for ovary development and their gut microbiota communities were characterized. The proportion of workers with developed ovaries was increased in the absence of QMP but also when fed a queen diet (royal jelly). Overall, we found that diet, rather than reproductive development or pheromone exposure, led to more "queen-like" microbiota in workers. However, we revealed that diet alone cannot explain the microbiota composition of workers. The hypothesis that reproductive development explains microbiota differences between queens and workers was rejected. We found evidence that diet is one of the main drivers of differences between the gut microbial community compositions of queens and workers but cannot fully explain the distinct microbiota of queens. Thus, we predict that behavioral and other physiological differences dictate microbiota composition in workers and queens. Our findings not only contribute to our understanding of the factors affecting the honey bee microbiota, which is important for bee health, but also illustrate the versatility and benefits of utilizing honeybees as a model system to study host-microbe interactions.

Anjali Zumkhawala-Cook

Patrick Gallagher

Kasie Raymann

Diet affects reproductive development and microbiota composition in honey bees

饮食影响蜜蜂的生殖发育和微生物群组成

Abstract Background Salmon aquaculture involves freshwater and seawater phases. Recently there has been an increase in multifactorial gill health challenges during the seawater phase which has led to an urgent need to understand the gill microbiome. There is a lack of understanding on what drives the composition of the gill microbiome, and the influence the freshwater stage has on its long-term composition. We characterise the gill microbiome from seven cohorts of Atlantic salmon raised in six different freshwater operational systems—recirculating aquaculture system (RAS), flowthrough (FT) and loch-based system, prior to and after transfer to seven seawater farms, over two different input seasons, S0 (2018) and S1 (2019). Results Using the V1-V2 region of the 16S rRNA gene, we produced amplicon libraries absent of host contamination. We showed that hatchery system influenced the gill microbiome (PERMAOVA R 2 = 0.226, p &lt; 0.001). Loch and FT systems were more similar to each other than the three RAS systems, which clustered together. On transfer to sea, the gill microbiomes of all fish changed and became more similar irrespective of the initial hatchery system, seawater farm location or season of input. Even though the gill microbiome among seawater farm locations were different between locations (PERMAOVA R 2 = 0.528, p &lt; 0.001), a clustering of the gill microbiomes by hatchery system of origin was still observed 7–25 days after transfer (PERMAOVA R = 0.164, p &lt; 0.001). Core microbiomes at genera level were observed among all fish in addition to freshwater only, and seawater only. At ASV level core microbiomes were observed among FT and loch freshwater systems only and among all seawater salmon. The gill microbiome and surrounding water at each hatchery had more shared ASVs than seawater farms. Conclusion We showed hatchery system, loch, FT or RAS, significantly impacted the gill microbiome. On transfer to sea, the microbiomes changed and became more similar. After transfer, the individual sites to which the fish were transferred has a significant influence on microbiome composition, but interesting some clustering by hatchery system remained. Future gill disease mitigation methods that target enhancing the gill microbiome may be most effective in the freshwater stage, as there were more shared ASVs between water and gill at hatchery, compared to at sea.

Kelly J. Stewart

Annette S. Boerlage

William Barr

Umer Z. Ijaz

Cindy J. Smith

Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea

孵化场类型影响大西洋养殖鲑鱼（Salmo salar）转移至海洋后的鳃微生物群

短名	anim microbiome
Journal Impact	4.74
国际分区	VETERINARY SCIENCES(Q1)

ISSN	2524-4671
h-index	22

涉及主题	生物遗传学化学生物化学医学地质学生态学古生物学生物信息学微生物群细菌基因免疫学微生物学动物肠道菌群内科学食品科学植物16S核糖体RNA有机化学病理
出版信息	出版商: BioMed Central Ltd，出版周期: ，期刊类型: journal，开源期刊: 是
基本数据	创刊年份: 2019，原创研究文献占比: 94.20%，自引率:6.10%， Gold OA占比: 100.00%
期刊费用	$2090详情
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Animal Microbiome

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Changes in social environment impact primate gut microbiota composition

Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea

The role of gut microbiota in a generalist, golden snub-nosed monkey, adaptation to geographical diet change

Diet affects reproductive development and microbiota composition in honey bees

Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea

Changes in social environment impact primate gut microbiota composition

Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea

The role of gut microbiota in a generalist, golden snub-nosed monkey, adaptation to geographical diet change

Diet affects reproductive development and microbiota composition in honey bees

Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea