Sociability in a non-captive macaque population is associated with beneficial gut bacteria

Associations among rearing environment and the infant gut microbiome with early-life neurodevelopment and cognitive development in a nonhuman primate model (Macaca mulatta)

Early gut microbiome development may impact brain and behavioral development. Using a nonhuman primate model (Macaca mulatta), we investigated the association between social environments and the gut microbiome on infant neurodevelopment and cognitive function. Infant rhesus monkeys (n = 33) were either mother-peer-reared (MPR) or nursery-reared (NR). Neurodevelopmental outcomes, namely emotional responsivity, visual orientation, and motor maturity, were assessed with the Primate Neonatal Neurobehavioral Assessment (PNNA) at 14-30 days. Cognitive development was assessed through tasks evaluating infant reward association, cognitive flexibility, and impulsivity at 6-8 months. The fecal microbiome was quantified from rectal swabs via 16S rRNA sequencing. Factor analysis was used to identify "co-abundance factors" describing patterns of microbial composition. We used multiple linear regressions with AIC Model Selection and differential abundance analysis (MaAsLin2) to evaluate relationships between co-abundance factors, microbiome diversity, and neuro-/cognitive development outcomes. At 30 days of age, a gut microbiome co-abundance factor, or pattern, with high Prevotella and Lactobacillus (β = -0.88, p = 0.04, AIC Weight = 68%) and gut microbiome alpha diversity as measured by Shannon diversity (β = -1.33, p = 0.02, AIC Weight = 80%) were both negatively associated with infant emotional responsivity. At 30 days of age, being NR was also associated with lower emotional responsivity (Factor 1 model: β = -3.13, p < 0.01; Shannon diversity model: β = -3.77, p < 0.01). The infant gut microbiome, along with early-rearing environments, may shape domains of neuro-/cognitive development related to temperament.

Gut microbiome strain-sharing within isolated village social networks

When humans assemble into face-to-face social networks, they create an extended social environment that permits exposure to the microbiome of others, thereby shaping the composition and diversity of the microbiome at individual and population levels1-6. Here we use comprehensive social network mapping and detailed microbiome sequencing data in 1,787 adults within 18 isolated villages in Honduras7 to investigate the relationship between network structure and gut microbiome composition. Using both species-level and strain-level data, we show that microbial sharing occurs between many relationship types, notably including non-familial and non-household connections. Furthermore, strain-sharing extends to second-degree social connections, suggesting the relevance of a person's broader network. We also observe that socially central people are more microbially similar to the overall village than socially peripheral people. Among 301 people whose microbiome was re-measured 2 years later, we observe greater convergence in strain-sharing in connected versus otherwise similar unconnected co-villagers. Clusters of species and strains occur within clusters of people in village social networks, meaning that social networks provide the social niches within which microbiome biology and phenotypic impact are manifested.

Extreme drought shapes the gut microbiota composition and function of common cranes (Grus grus) wintering in Poyang Lake

Introduction

Extreme weather events driven by climate change profoundly affect migratory birds by altering their habitats, food sources, and migration routes. While gut microbiota is believed to play a role in helping birds adapt to environmental changes, research on how extreme weather impacts their gut microbiota and how these microbial communities respond to such conditions has been limited.

Methods

16S rRNA gene sequencing was utilized to investigate the gut microbiota of common cranes (Grus grus) wintering at Poyang Lake from 2020 to 2023, with a particular focus on their response to extreme drought conditions on both inter-annual and monthly timescales.

Results

The results revealed that extreme drought conditions substantially impact gut microbiota, with inter-annual water-level fluctuations exerting a more pronounced impact on microbial community structure than that of inter-monthly fluctuations. Notably, a significant decline in bacterial diversity within the gut microbiota of common cranes was observed in the extreme drought year of 2022 compared with other years. Monthly observations indicated a gradual increase in gut microbial diversity, coinciding with relatively minor water-level changes. Key taxa that responded to drought included the Enterobacteriaceae family and Bifidobacterium and Lactobacillus species. Additionally, functional genes related to carbohydrate metabolism, the phosphotransferase system, and the two-component systems were significantly enriched during the extreme drought year. These functions may represent adaptive mechanisms by which the gut microbiota of common cranes respond to drought stress.

Discussion

This research provides novel insights into the temporal variability of gut microbiota in wintering waterbirds, underscoring the significant impact of climatic fluctuations on microbial communities. The findings highlight the importance of understanding the ecological and functional responses of gut microbiota to extreme weather events, which is crucial for the conservation and management of migratory bird populations in the face of climate change.

Changes in social environment impact primate gut microbiota composition

BACKGROUND

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.

RESULTS

We performed a 15-month longitudinal investigation wherein we disentangled the impacts of diet and social living conditions on GM composition in a captive cohort of 13 male cynomolgus macaques. The animals were in single housing for the first 3 months of the study initially with a variable diet. After baseline data collection they were placed on a controlled diet for the remainder of the study. Following this diet shift the animals were moved to paired housing for 6 months, enabling enhanced social interaction, and then subsequently returned to single housing at the end of our study. This structured sequencing of diet and housing changes allowed us to assess their distinct impacts on GM composition. We found that the early dietary adjustments led to GM changes in both alpha and beta diversity, whereas changes in social living conditions only altered beta diversity. With respect to the latter, we found that two particular bacterial families - Lactobacillaceae and Clostridiaceae - demonstrated significant shifts in abundance during the transition from single housing to paired housing, which was distinct from the shifts we observed based on a change in diet. Conversely, we found that other bacteria previously associated with sociality were not altered based on changes in social living conditions but rather only by changes in diet.

CONCLUSIONS

Together, these findings decouple the influences that diet and social living have on GM composition and reconcile previous observations in the human and animal literatures. Moreover, the results indicate biological alterations of the gut that may, in part, mediate the relationship between sociality and wellbeing.

Evolution and the critical role of the microbiota in the reduced mental and physical health associated with low socioeconomic status (SES)

The evolution of the gut-microbiota-brain axis in animals reveals that microbial inputs influence metabolism, the regulation of inflammation and the development of organs, including the brain. Inflammatory, neurodegenerative and psychiatric disorders are more prevalent in people of low socioeconomic status (SES). Many aspects of low SES reduce exposure to the microbial inputs on which we are in a state of evolved dependence, whereas the lifestyle of wealthy citizens maintains these exposures. This partially explains the health deficit of low SES, so focussing on our evolutionary history and on environmental and lifestyle factors that distort microbial exposures might help to mitigate that deficit. But the human microbiota is complex and we have poor understanding of its functions at the microbial and mechanistic levels, and in the brain. Perhaps its composition is more flexible than the microbiota of animals that have restricted habitats and less diverse diets? These uncertainties are discussed in relation to the encouraging but frustrating results of attempts to treat psychiatric disorders by modulating the microbiota.

A gut (microbiome) feeling about addiction: Interactions with stress and social systems

In recent years, an increasing attention has given to the intricate and diverse connection of microorganisms residing in our gut and their impact on brain health and central nervous system disease. There has been a shift in mindset to understand that drug addiction is not merely a condition that affects the brain, it is now being recognized as a disorder that also involves external factors such as the intestinal microbiota, which could influence vulnerability and the development of addictive behaviors. Furthermore, stress and social interactions, which are closely linked to the intestinal microbiota, are powerful modulators of addiction. This review delves into the mechanisms through which the microbiota-stress-immune axis may shape drug addiction and social behaviors. This work integrates preclinical and clinical evidence that demonstrate the bidirectional communication between stress, social behaviors, substance use disorders and the gut microbiota, suggesting that gut microbes might modulate social stress having a significance in drug addiction.

The Profound Influence of Gut Microbiome and Extracellular Vesicles on Animal Health and Disease

The animal gut microbiota, comprising a diverse array of microorganisms, plays a pivotal role in shaping host health and physiology. This review explores the intricate dynamics of the gut microbiome in animals, focusing on its composition, function, and impact on host-microbe interactions. The composition of the intestinal microbiota in animals is influenced by the host ecology, including factors such as temperature, pH, oxygen levels, and nutrient availability, as well as genetic makeup, diet, habitat, stressors, and husbandry practices. Dysbiosis can lead to various gastrointestinal and immune-related issues in animals, impacting overall health and productivity. Extracellular vesicles (EVs), particularly exosomes derived from gut microbiota, play a crucial role in intercellular communication, influencing host health by transporting bioactive molecules across barriers like the intestinal and brain barriers. Dysregulation of the gut-brain axis has implications for various disorders in animals, highlighting the potential role of microbiota-derived EVs in disease progression. Therapeutic approaches to modulate gut microbiota, such as probiotics, prebiotics, microbial transplants, and phage therapy, offer promising strategies for enhancing animal health and performance. Studies investigating the effects of phage therapy on gut microbiota composition have shown promising results, with potential implications for improving animal health and food safety in poultry production systems. Understanding the complex interactions between host ecology, gut microbiota, and EVs provides valuable insights into the mechanisms underlying host-microbe interactions and their impact on animal health and productivity. Further research in this field is essential for developing effective therapeutic interventions and management strategies to promote gut health and overall well-being in animals.

Microbial transmission in the social microbiome and host health and disease

Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.

New methods to unveil host-microbe interaction mechanisms along the microbiota-gut-brain-axis

Links between the gut microbiota and human health have been supported throughout numerous studies, such as the development of neurological disease disorders. This link is referred to as the "microbiota-gut-brain axis" and is the focus of an emerging field of research. Microbial-derived metabolites and gut and neuro-immunological metabolites regulate this axis in health and many diseases. Indeed, assessing these signals, whether induced by microbial metabolites or neuro-immune mediators, could significantly increase our knowledge of the microbiota-gut-brain axis. However, this will require the development of appropriate techniques and potential models. Methods for studying the induced signals originating from the microbiota remain crucial in this field. This review discusses the methods and techniques available for studies of microbiota-gut-brain interactions. We highlight several much-debated elements of these methodologies, including the widely used in vivo and in vitro models, their implications, and perspectives in the field based on a systematic review of PubMed. Applications of various animal models (zebrafish, mouse, canine, rat, rabbit) to microbiota-gut-brain axis research with practical examples of in vitro methods and innovative approaches to studying gut-brain communications are highlighted. In particular, we extensively discuss the potential of "organ-on-a-chip" devices and their applications in this field. Overall, this review sheds light on the most widely used models and methods, guiding researchers in the rational choice of strategies for studies of microbiota-gut-brain interactions.

The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal

The gut microbiome has a well-documented relationship with host fitness. Greater microbial diversity and abundance of specific microbes have been associated with improved fitness outcomes. Intestinal microbes also may be associated with patterns of social behaviour. However, these associations have been largely studied in captive animal models; we know less about microbiome composition as a potential driver of individual social behaviour and position in the wild. We used linear mixed models to quantify the relationship between fecal microbial composition, diversity and social network traits in a wild population of yellow-bellied marmots (Marmota flaviventer). We focused our analyses on microbes previously linked to sociability and neurobehavioural alterations in captive rodents, primates and humans. Using 5 years of data, we found microbial diversity (Shannon-Wiener and Faith's phylogenetic diversity) has a modest yet statistically significant negative relationship with the number of social interactions an individual engaged in. We also found a negative relationship between Streptococcus spp. relative abundance and two social network measures (clustering coefficient and embeddedness) that quantify an individual's position relative to others in their social group. These findings highlight a potentially consequential relationship between microbial composition and social behaviour in a wild social mammal.

Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac

MOTIVATION

Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely used metric for measuring the variability between metagenomic samples. We propose that the characterization of metagenomic environments can be improved by finding the average, a.k.a. the barycenter, among the samples with respect to the UniFrac distance. However, it is possible that such a UniFrac-average includes negative entries, making it no longer a valid representation of a metagenomic community.

RESULTS

To overcome this intrinsic issue, we propose a special version of the UniFrac metric, termed L2UniFrac, which inherits the phylogenetic nature of the traditional UniFrac and with respect to which one can easily compute the average, producing biologically meaningful environment-specific "representative samples." We demonstrate the usefulness of such representative samples as well as the extended usage of L2UniFrac in efficient clustering of metagenomic samples, and provide mathematical characterizations and proofs to the desired properties of L2UniFrac.

AVAILABILITY AND IMPLEMENTATION

A prototype implementation is provided at https://github.com/KoslickiLab/L2-UniFrac.git. All figures, data, and analysis can be reproduced at https://github.com/KoslickiLab/L2-UniFrac-Paper.

The Effects of Social Experience on Host Gut Microbiome in Male Zebrafish (Danio rerio)

AbstractAlthough the gut and the brain vastly differ in physiological function, they have been interlinked in a variety of different neurological and behavioral disorders. The bacteria that comprise the gut microbiome communicate and influence the function of various physiological processes within the body, including nervous system function. However, the effects of social experience in the context of dominance and social stress on gut microbiome remain poorly understood. Here, we examined whether social experience impacts the host zebrafish (Danio rerio) gut microbiome. We studied how social dominance during the first 2 weeks of social interactions changed the composition of zebrafish gut microbiome by comparing gut bacterial composition, diversity, and relative abundance between socially dominant, submissive, social isolates and control group-housed communal fish. Using amplicon sequencing of the 16S rRNA gene, we report that social dominance significantly affects host gut bacterial community composition but not bacterial diversity. At the genus level, Aeromonas and unclassified Enterobacteriaceae relative abundance decreased in dominant individuals while commensal bacteria (e.g., Exiguobacterium and Cetobacterium) increased in relative abundance. Conversely, the relative abundance of Psychrobacter and Acinetobacter was increased in subordinates, isolates, and communal fish compared to dominant fish. The shift in commensal and pathogenic bacteria highlights the impact of social experience and the accompanying stress on gut microbiome, with potentially similar effects in other social organisms.

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L 2 UniFrac

Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely-used metric for measuring the variability between metagenomic samples. We propose that the characterization of metagenomic environments can be achieved by finding the average, a.k.a. the barycenter, among the samples with respect to the UniFrac distance. However, it is possible that such a UniFrac-average includes negative entries, making it no longer a valid representation of a metagenomic community. To overcome this intrinsic issue, we propose a special version of the UniFrac metric, termed L ₂ UniFrac, which inherits the phylogenetic nature of the traditional UniFrac and with respect to which one can easily compute the average, producing biologically meaningful environment-specific "representative samples". We demonstrate the usefulness of such representative samples as well as the extended usage of L ₂ UniFrac in efficient clustering of metagenomic samples, and provide mathematical characterizations and proofs to the desired properties of L ₂ UniFrac. A prototype implementation is provided at: https://github.com/KoslickiLab/L2-UniFrac.git .