The gut microbiome as a driver of individual variation in cognition and functional behaviour

Research into proximate and ultimate mechanisms of individual cognitive variation in animal populations is a rapidly growing field that incorporates physiological, behavioural and evolutionary investigations. Recent studies in humans and lab animals have shown that the enteric microbial community plays a central role in brain development and functioning. The ‘gut-brain axis’ represents a multi-directional signalling system that encompasses neurological, immunological and hormonal pathways. In particular it is tightly linked with the hypothalamic-pituitary-adrenal axis (HPA), a system that regulates stress hormone release, and influences brain development and function. Experimental examination of the microbiome through manipulation of diet, infection, stress and exercise, suggests direct effects on cognition, including learning and memory. However, our understanding of these processes in natural populations is extremely limited. Here we outline how recent advances in predominantly laboratory-based microbiome research can be applied to understanding individual differences in cognition. Experimental manipulation of the microbiome across natal and adult environments will help to unravel the interplay between cognitive variation and the gut microbial community. Focus on individual variation in the gut microbiome and cognition in natural populations will reveal new insight into the environmental and evolutionary constraints that drive individual cognitive variation.

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The gut microbiome as a driver of individual variation in cognition and functional behaviour

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2017.0286 ◽

2018 ◽

Vol 373 (1756) ◽

pp. 20170286 ◽

Cited By ~ 28

Author(s):

Gabrielle L. Davidson ◽

Amy C. Cooke ◽

Crystal N. Johnson ◽

John L. Quinn

Keyword(s):

Individual Differences ◽

Microbial Community ◽

Individual Variation ◽

Gut Microbiome ◽

Cognitive Abilities ◽

Natural Populations ◽

Experimental Manipulation ◽

Laboratory Animals ◽

Animal Populations ◽

And Function

Research into proximate and ultimate mechanisms of individual cognitive variation in animal populations is a rapidly growing field that incorporates physiological, behavioural and evolutionary investigations. Recent studies in humans and laboratory animals have shown that the enteric microbial community plays a central role in brain function and development. The ‘gut–brain axis’ represents a multi-directional signalling system that encompasses neurological, immunological and hormonal pathways. In particular it is tightly linked with the hypothalamic–pituitary–adrenal axis (HPA), a system that regulates stress hormone release and influences brain development and function. Experimental examination of the microbiome through manipulation of diet, infection, stress and exercise, suggests direct effects on cognition, including learning and memory. However, our understanding of these processes in natural populations is extremely limited. Here, we outline how recent advances in predominantly laboratory-based microbiome research can be applied to understanding individual differences in cognition. Experimental manipulation of the microbiome across natal and adult environments will help to unravel the interplay between cognitive variation and the gut microbial community. Focus on individual variation in the gut microbiome and cognition in natural populations will reveal new insight into the environmental and evolutionary constraints that drive individual cognitive variation. This article is part of the theme issue ‘Causes and consequences of individual differences in cognitive abilities’.

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The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

Scientific Reports ◽

10.1038/s41598-021-95146-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Judith Mogouong ◽

Philippe Constant ◽

Pierre Legendre ◽

Claude Guertin

Keyword(s):

Microbial Community ◽

Gut Microbiome ◽

Strong Predictor ◽

Emerald Ash Borer ◽

Agrilus Planipennis ◽

Food Sources ◽

Microbiome Composition ◽

Living Organisms ◽

Insect Gut ◽

Gut Microbial Community

AbstractThe microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

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Brain Aging and Gut–Brain Axis

Nutrients ◽

10.3390/nu11020424 ◽

2019 ◽

Vol 11 (2) ◽

pp. 424 ◽

Cited By ~ 1

Author(s):

M. Mohajeri

Keyword(s):

Multiple Sclerosis ◽

Alzheimer’S Disease ◽

Parkinson’S Disease ◽

Alzheimer's Disease ◽

Parkinson's Disease ◽

Brain Development ◽

Neurodegenerative Disorders ◽

Gut Microbiome ◽

Brain Aging ◽

And Function

In the last decade, the microbiome in general and the gut microbiome in particular have been associated not only to brain development and function, but also to the pathophysiology of brain aging and to neurodegenerative disorders such as Alzheimer’s disease (AD), Parkinson’s disease (PD), depression, or multiple sclerosis (MS) [...]

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Microorganisms in the human gut: Diversity and function

The Biochemist ◽

10.1042/bio03304004 ◽

2011 ◽

Vol 33 (4) ◽

pp. 4-9

Author(s):

Karen P. Scott ◽

Sylvia H. Duncan ◽

Petra Louis ◽

Harry J. Flint

Keyword(s):

Microbial Community ◽

Structure And Function ◽

Interindividual Variation ◽

Healthy Individuals ◽

Human Gastrointestinal Tract ◽

Human Gut ◽

Current State ◽

And Function ◽

Micro Organisms ◽

Gut Microbial Community

Research into the microbial community within the human gastrointestinal tract (GIT) has developed from investigating micro-organisms that cause disease to trying to establish those that are important to maintain health. Thus we are now at a point where the bacterial community in healthy individuals has been well characterized, emphasizing the huge interindividual variation that exists. Molecular advances have also facilitated initial studies on establishing the composition of the viral and eukaryotic communities. In this article, we provide an overview of the current state of knowledge, illustrating the structure and function of the gut microbial community.

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Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.0955 ◽

2017 ◽

Vol 284 (1862) ◽

pp. 20170955 ◽

Cited By ~ 24

Author(s):

Qi Wu ◽

Xiao Wang ◽

Yun Ding ◽

Yibo Hu ◽

Yonggang Nie ◽

...

Keyword(s):

Gut Microbiome ◽

Cell Cycle Control ◽

Nutrient Utilization ◽

Giant Pandas ◽

Microbiome Composition ◽

Leaf Stage ◽

Bamboo Shoots ◽

And Function ◽

Gut Microbial Community ◽

Metagenomic Approach

Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different. Functional metagenomic analysis showed that in the leaf stage, bacteria species over-represented genes involved in raw fibre utilization and cell cycle control. Thus, raw fibre utilization by the gut microbiome was guaranteed during the nutrient-deficient leaf stage by reinforcing gut microbiome robustness. During the protein-abundant shoot stage, the functional capacity of the gut microbiome expanded to include prokaryotic secretion and signal transduction activity, suggesting active interactions between the gut microbiome and host. These results illustrate that seasonal nutrient variation in wild giant pandas substantially influences gut microbiome composition and function. Nutritional interactions between gut microbiomes and hosts appear to be complex and further work is needed.

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Differences in Gut Microbiome Composition Between Sympatric Wild and Allopatric Laboratory Populations of Omnivorous Cockroaches

Frontiers in Microbiology ◽

10.3389/fmicb.2021.703785 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kara A. Tinker ◽

Elizabeth A. Ottesen

Keyword(s):

Microbial Community ◽

Gut Microbiome ◽

Periplaneta Americana ◽

Laboratory Environment ◽

Microbiome Composition ◽

Relative Contribution ◽

Microbiome Diversity ◽

Before And After ◽

Laboratory Populations ◽

Gut Microbial Community

Gut microbiome composition is determined by a complex interplay of host genetics, founder’s effects, and host environment. We are using omnivorous cockroaches as a model to disentangle the relative contribution of these factors. Cockroaches are a useful model for host–gut microbiome interactions due to their rich hindgut microbial community, omnivorous diet, and gregarious lifestyle. In this study, we used 16S rRNA sequencing to compare the gut microbial community of allopatric laboratory populations of Periplaneta americana as well as sympatric, wild-caught populations of P. americana and Periplaneta fuliginosa, before and after a 14 day period of acclimatization to a common laboratory environment. Our results showed that the gut microbiome of cockroaches differed by both species and rearing environment. The gut microbiome from the sympatric population of wild-captured cockroaches showed strong separation based on host species. Laboratory-reared and wild-captured cockroaches from the same species also exhibited distinct gut microbiome profiles. Each group of cockroaches had a unique signature of differentially abundant uncharacterized taxa still present after laboratory cultivation. Transition to the laboratory environment resulted in decreased microbiome diversity for both species of wild-caught insects. Interestingly, although laboratory cultivation resulted in similar losses of microbial diversity for both species, it did not cause the gut microbiome of those species to become substantially more similar. These results demonstrate how competing factors impact the gut microbiome and highlight the need for a greater understanding of host–microbiome interactions.

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Host Habitat Is the Major Determinant of the Gut Microbiome of Fish

10.21203/rs.3.rs-332643/v1 ◽

2021 ◽

Author(s):

Pil Soo Kim ◽

Na-Ri Shin ◽

Jae-Bong Lee ◽

Min-Soo Kim ◽

Tae Woong Whon ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Gut Microbiome ◽

Microbial Community Composition ◽

Terrestrial Vertebrates ◽

Symbiotic Relationships ◽

Machine Learning Approach ◽

Host Habitat ◽

Functional Profiles ◽

Gut Microbial Community

Abstract Background: Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish.Results: We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).Conclusions: Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds.

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Bacteriophages in Gut Microbiome Interactions in Patients with Inflammatory Bowel Disease: Differences by Sex and The Disease Type

10.21203/rs.3.rs-1240997/v1 ◽

2022 ◽

Author(s):

Fatemeh Farahmandzad ◽

Hossein Lanjanian ◽

Ehsan Arefian ◽

Kaveh Kavousi

Keyword(s):

Ulcerative Colitis ◽

Inflammatory Bowel Disease ◽

Crohn’S Disease ◽

Microbial Community ◽

Crohn's Disease ◽

Bowel Disease ◽

Gut Microbiome ◽

Disease Type ◽

Inflammatory Bowel ◽

Gut Microbial Community

Abstract Background: Inflammatory bowel disease (IBD), known as the disease of the century, is a complex condition that affects millions of people worldwide. IBD is influenced by numerous factors such as genetics, lifestyle, and the gut microbial community, yet the role of microorganisms in driving and controlling the disease remains poorly understood. As we know, preceding studies have mainly focused on assessing gut bacteria and less on bacteriophages or fungi, and no study on interactions of the gut microbial community in patients with IBD has looked at bacteriophages in addition to bacteria and fungi by sex. No distinct microbial regulatory candidate has been proposed so far.Results: Here, metagenomic data were obtained from 456 stool samples of 84 white race volunteers (40 females and 44 males) with no treatment history before sampling. Participants were studied by sex and the disease type using bioinformatics methods. Differences in interactions of bacteriophages, bacteria, fungi, and archaea in the gut of males and females with Crohn's disease were remarkable, indicating the necessity for different therapies for both groups. While, little difference was seen in the gut microbiome relations in females and males with ulcerative colitis.Conclusions: The fungal strain Malassezia globose CBS 7966 beside the bacterial species Bacteroides stercorisin ulcerative colitis and Parabacteroides phage YZ-2015b in Crohn's disease were the sex-independent regulatory candidates. Uncultured crAssphage was recommended as a sex-dependent regulatory candidate for IBD in men. However, the fungus Wickerhamomycesciferrii which had proposed as regulatory candidate in Crohn's disease, was age-dependent in females. Four bacteriophages, such as Escherichia phage pro147, were suggested for study candidates in the metabolism of IBD.

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Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples

Scientific Reports ◽

10.1038/s41598-018-22408-4 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 26

Author(s):

Roshonda B. Jones ◽

Xiangzhu Zhu ◽

Emili Moan ◽

Harvey J. Murff ◽

Reid M. Ness ◽

...

Keyword(s):

Microbial Community ◽

Individual Variation ◽

Rectal Swab ◽

Community Assessment ◽

Gut Microbial Community

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The Gut Microbiota composition of Feral and Tamworth Pigs determined using High-Throughput Culturomics and Metagenomics Reveals Compositional Variations When Compared to the Commercial Breeds

10.1101/738278 ◽

2019 ◽

Author(s):

Gavin J. Fenske ◽

Sudeep Ghimire ◽

Linto Antony ◽

Jane Christopher-Hennings ◽

Joy Scaria

Keyword(s):

Gut Microbiome ◽

Natural Populations ◽

Antibiotic Resistance Genes ◽

Distinct Species ◽

Culture Techniques ◽

Microbiome Composition ◽

Modern Agriculture ◽

Compositional Variations ◽

And Function ◽

Pig Microbiome

AbstractBacterial communities in the hindguts of pigs have a profound impact on health and disease. Yet very limited studies have been performed outside intensive swine farms to determine pig gut microbiome composition in natural populations. Feral pigs represent a unique situation where the microbiome structure can be observed outside the realm of modern agriculture. Additionally, Tamworth pigs that freely forage were included to characterize the microbiome structure of this rare breed. In this study, gut microbiome of feral and Tamworth pigs were determined using metagenomics and culturomics. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. In total, 46 distinct species were successfully isolated from 1000 colonies selected. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. Furthermore, the naturally raised Tamworth pig microbiome contained more number of antibiotic resistance genes when compared to feral pig microbiome. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function by assembling simple to complex microbiota communities in bioreactors or germfree animal models.

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