Biology subjects

Bjork, J. R.

Publications and source records attributed to Bjork, J. R..

5 recordsLinked to original sources

bioRxiv2021

Synchrony and idiosyncrasy in the gut microbiome of wild primates

Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments, and medications, but it could also emerge from fundamental ecological forces that shape microbiota more generally. Here we leverage extensive gut microbial time series from wild baboons--hosts who experience little interindividual dietary and environmental heterogeneity--to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, baboon microbiome dynamics were only weakly synchronized. The strongest synchrony occurred among baboons living in the same social group, likely because group members range over the same habitat and simultaneously encounter the same sources of food and water. However, this synchrony was modest compared to each hosts personalized dynamics. Indeed, host-specific factors, especially host identity, explained 10 times the deviance in longitudinal microbial dynamics, compared to factors shared across hosts. These results contribute to mounting evidence that highly idiosyncratic gut microbiomes are not an artifact of modern human environments, and that synchronizing forces in the gut microbiome (e.g., shared environments, diets, and microbial dispersal) are often not strong enough to overwhelm drivers of microbiome personalization, including host genetics, priority effects, horizontal gene transfer, and functional redundancy.

ecology↗

bioRxiv2020

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

The gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We then correlated this to 241 host and environmental factors, including physical and mental health, medication use, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is primarily shaped by environment and cohousing. Only [~]13% of taxa are heritable, which are enriched with highly prevalent and health-associated bacteria. By identifying 2,856 associations between microbiome and health, we find that seemingly unrelated diseases share a common signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, of which numerous early-life and current factors are particularly linked to the microbiome. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.

microbiology↗

bioRxiv2018

Vertical transmission of sponge microbiota is weak and inconsistent

Classic coevolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Here, we test these ideas for the first time in multiple coexisting host species with highly diverse microbiota, leveraging known parent-offspring pairs sampled from eight species of wild marine sponges (Porifera). We found that the processes governing vertical transmission were both neutral and selective. A neutral model explained 66% of the variance in larval microbiota, which was higher than the variance this model explained for adult sponge microbiota (R2 = 27%). However, microbes that are enriched above neutral expectations in adults were disproportionately transferred to offspring. Patterns of vertical transmission were, however, incomplete: larval sponges shared, on average, 44.8% of microbes with their parents, which was not higher than the fraction they shared with nearby non-parental adults. Vertical transmission was also inconsistent across siblings, as larval sponges from the same parent only shared 17% of microbes. Finally, we found no evidence that vertically transmitted microbes are faithful to a single sponge host species. Surprisingly, larvae were just as likely to share vertically transmitted microbes with larvae from other sponge species as they were with their own species. Our study demonstrates that common predictions of vertical transmission that stem from species-poor systems are not necessarily true when scaling up to diverse and complex microbiomes.

ecology↗

bioRxiv2017

The Dynamic Core Microbiome: Structure, Stability And Resistance

The long-term stability of microbiomes is crucial as the persistent occurrence of beneficial microbes and their associated functions ensure host health and well-being. Microbiomes are highly diverse and dynamic, making them challenging to understand. Because many natural systems work as temporal networks, we present an approach that allows identifying meaningful ecological patterns within complex microbiomes: the dynamic core microbiome. On the basis of six marine sponge species sampled monthly over three years, we study the structure, dynamics and stability of their microbiomes. What emerge for each microbiome is a negative relationship between temporal variability and mean abundance. The notion of the dynamic core microbiome allowed us to determine a relevant functional attribute of the microbiome: temporal stability is not determined by the diversity of a hosts microbial assemblages, but rather by the density of those microbes that conform its core microbiome. The core microbial interaction network consisted of complementary members interacting weakly with dominance of comensal and amensal interactions that suggests self-regulation as a key determinant of the temporal stability of the microbiome. These interactions have likely coevolved to maintain host functionality and fitness over ecological, and even evolutionary time scales.

ecology↗

bioRxiv2017

Uncovering The Drivers Of Animal-Host Microbiotas With Joint Distribution Modeling

In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure, and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates like diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including: (i) model-based ordination to visualize and quantify the main patterns in the data; (ii) variance partitioning to asses how influential the included host-specific factors are in structuring the microbiota; and (iii) co-occurrence networks to visualize microbe-to-microbe associations.

microbiology↗