Biology subjects

Gilbert, J. A.

Publications and source records attributed to Gilbert, J. A..

At least 19 recordsLinked to original sources

bioRxiv2026

Soil microbial inoculants augment fertilizer performance across contrasting cropping systems in Rwanda

Smallholder farming systems in sub-Saharan Africa are constrained by declining soil fertility, erosion, and rising fertilizer costs, creating an urgent need for scalable inputs that sustain yields while maintaining soil health. While there is some evidence that microbial inoculants may offer a promising complement to conventional fertility management, field-scale evidence in tropical cereal and tuber systems remains limited. Here, we evaluated a multi-species inoculant composed of 20-22 Bacillus and Streptomyces species on potato and maize across four sites in Rwanda over two growing seasons (2025A and 2025B). Treatments included the inoculant applied at two rates (150 and 250 g ha-1), both alone and in combination with standard fertilization (inorganic fertilizer plus manure), alongside untreated and fertilized controls. Co-application of the inoculant with standard fertilization increased yield and plant biomass beyond fertilization alone, with gains of 6-51% for maize and 3-58% for potato. However, while the inoculant applied alone outperformed untreated controls, it generally did not match standard fertilization. Responses were strongest and most consistent for large-grade potato tubers, and application rate interacted with crop type, whereby the lower dose maximized marketable tuber yield, while maize showed a positive dose-response for grain and biomass. Yield increases were not accompanied by reductions in crop nutrient density, which was instead governed by site-level differences. Altogether, these results indicate that multi-species microbial inoculants are an effective complement to existing fertility practices that may offer, pending further research, a potential pathway to partial fertilizer replacement while sustaining productivity and nutritional quality in smallholder tropical agriculture.

ecology↗

bioRxiv2026

Complex microbial consortia improve yield and physiological performance of leafy greens under deficit irrigation

O_LIWater scarcity is an increasing constraint on agricultural productivity, particularly for high-value vegetable crops. Deficit irrigation strategies can reduce water use but frequently compromise yield and crop physiological status. Scalable, biologically based tools are needed to sustain crop performance under reduced water input without reliance on additional agrochemical inputs. C_LIO_LIFive functionally diverse microbial consortia were assembled from taxa selected to support rhizosphere colonization, soil structural stabilization, and fungal-mediated nutrient and water foraging. Consortia were evaluated in greenhouse trials with lettuce (Lactuca sativa) and spinach (Spinacia oleracea) grown under full irrigation or a 30% deficit irrigation regime (70% of crop water requirement). Crop responses were assessed using yield, harvest delay, root length, wilting incidence, chlorophyll content, and Water Band Index. C_LIO_LIAcross both crops, microbial consortium treatments improved performance under deficit irrigation relative to untreated water-stressed controls. In lettuce, yield increased by 3-9%; in spinach, yield increased by 4-13%, with several treatments restoring performance to levels not significantly different from fully irrigated controls. C_LIO_LIMicrobial treatments reduced harvest delay by an average of three to four days, improved root length, lowered wilting incidence, and reduced WBI, indicating attenuation of plant water stress. In several cases, physiological responses under deficit irrigation approached those observed under full irrigation despite 30% lower water input. Higher application rates generally produced stronger responses, though this trend was not always statistically significant. C_LIO_LISynthesis and applications. Complex microbial consortia can buffer the physiological and yield penalties of deficit irrigation in leafy green crops. These findings demonstrate the potential of soil microbiome-based inoculants as scalable, biologically derived tools to improve agricultural water-use efficiency and resilience under increasing water scarcity. Practical adoption of such consortia could reduce irrigation demand in intensive vegetable production systems without proportional yield loss, supporting both economic and environmental sustainability goals in water-limited agricultural contexts. C_LI

microbiology↗

bioRxiv2026

A high fermentable fiber Western diet reduces indole levels

Changes in gut microbiota composition due to diet impact health. Fiber-rich diets promote beneficial microbiota and reduce the risk of metabolic diseases, while low-fiber, calorie-dense diets are linked to dysbiosis and increased disease risk. This study examines the effects of a Western diet (WD) and explores dietary fiber supplements as potential modifiers of those effects. 10-week-old C57Bl/6J male mice were fed control (low-fat) or WD (high-fat, high-sucrose) containing 0% fermentable fiber (FF) or WD supplemented with 20% FF (fructooligosaccharides, FOS; guar gum, GG, or pectin, Pec). After 19 weeks, analysis of the cecal metagenome using whole-genome shotgun sequencing, metabolome by untargeted and targeted LC-MS/MS, and tissue RNA and protein expression by RT-PCR and immunoblotting was undertaken. WD-FF reduced metabolic derangements from WD while also improving GM diversity and altering cecal metabolites, particularly tryptophan metabolism. A profound increase in cecal indole levels (targeted metabolomics) was noted in WD vs WD-FF groups. As the primary indole-oxidizing enzyme, CYP2E1 generates indoxyl sulfate, which contributes to oxidative stress and a leaky gut. Mice on WD displayed higher expression of Cyp2e1 mRNA in the gut. In the liver, the levels of both CYP2E1 protein and mRNA were higher in the WD group compared to the WD-FOS group, with protein levels also higher than in the WD-Pec group and mRNA levels higher than in the WD-GG group. mRNA expression of markers of oxidative stress, inflammation, and leaky barrier was significantly higher in the liver and intestine of the WD vs the WD-FF groups. FFs reduced high plasma indoxyl sulfate levels (except in WD-GG), and boosted short-chain fatty acids and indole acetic acid. Our data suggest that WD disrupts GM tryptophan metabolism, possibly by altering the balance between indole-producing and utilizing gut bacteria. Dietary fiber supplementation exerts protective effects, in part, by mitigating this imbalance.

physiology↗

bioRxiv2026

Environmental Fungi Modulate the Vaginal Mycobiome and Cervical Disease Progression in Hispanic Women

The vaginal mycobiome, though a minor component of the cervicovaginal ecosystem, plays a crucial role in reproductive health and disease. However, its composition and interactions with bacterial communities remain poorly understood, particularly among Hispanic women, who experience disproportionately high rates of Human papillomavirus (HPV) infection and cervical cancer. We characterized the vaginal mycobiota across reproductive stages and examined its associations with cervical disease, HPV status, and bacterial community state types (CSTs) in 86 Hispanic participants from Puerto Rico using ITS1 amplicon sequencing. Amplicon sequence variants were inferred with QIIME2/DADA2 and taxonomically classified using the UNITE database, with diversity and discriminant taxa analyses applied to explore clinical and microbial associations. We detected 173 fungal Species Hypotheses, dominated by Candida albicans, Agaricomycetes sp., Scopuloides dimorpha, and Hortaea werneckii. While fungal composition did not differ significantly by reproductive stage, non-pregnant individuals exhibited greater inter-individual variability. Alpha diversity was reduced in high-grade squamous intraepithelial lesions compared with low-grade or normal cytology, and Candida parapsilosis prevalence was elevated in low-grade lesions. CST III, characterized by Lactobacillus iners dominance, showed greater dispersion variance than other CSTs. Collectively, these findings reveal a diverse vaginal mycobiome with stage- and disease-specific features, and a notable contribution of environmental fungi that may influence cervical pathogenesis. This work provides foundational insight into cervicovaginal fungal ecology in a high-risk Hispanic population and highlights the importance of integrating bacteriome-mycobiome analyses in womens health research.

microbiology↗

bioRxiv2026

My Gut Feels Your Pain - The Social Transfer of Pain Remodels the Gut Microbiome

BackgroundThe "social transfer of pain" is a phenomenon where a mouse experiencing injury-induced hyperalgesia can trigger hyperalgesia in a mouse briefly housed in the same environment ( bystander). The peripheral mechanisms underlying social transfer of pain in mice are not yet well described. As gut microbes are associated with social interactions, pain states, and pain attenuation via the gut-brain axis, we hypothesized that the bystander gut microbiome may respond to the social transfer of pain. MethodsTo induce the social transfer of pain, complete Freunds adjuvant (CFA) was injected into the hindpaw of a mouse which then underwent social interaction with a bystander for one hour. Mechanical sensitivity was assessed using the Von Frey mechanical sensitivity test. Stool samples and mechanical thresholds were taken prior to social interaction, 4 hours post-social interaction, and 24 hours post-social interaction. Metagenomic sequencing characterized the taxonomic and predicted functional gene response of the gut microbiome to CFA-induced pain, social transfer of pain and control groups. ResultsAt 4 hours post-social interaction, bystander animals experienced increased mechanical sensitivity comparable to CFA-injected animals and significantly lower than controls, indicating enhanced hyperalgesia. Compared to baseline, fecal community composition analyses at 4 hours and 24 hours post-interaction showed significant differences in Unweighted Unifrac in both CFA-injected and bystander animals but not in controls. Differential abundance analyses using Maaslin2 identified significant increases in the relative abundances of short chain fatty acid producing taxa like Lachnospiraceae, Ruminococcaceae, Oscillospiraceae and decreases in commensal mouse gut microbes like Muribaculaceae from baseline to 4 hours and 24 hours post-interaction in both bystanders and CFA-injected animals but not in controls. Functional analysis revealed increased abundance of pathways related to short-chain fatty acid production including pyruvate to butanoate and L-lysine fermentation to acetate and butanoate. The altered gut microbiome of bystanders strongly resembles that observed in CFA-injected animals at 4 hours and 24 hours post-injection, with the addition of a unique bystander bloom in several species of Lachnospiraceae. ConclusionsThe changes in the gut microbiome of bystander animals suggest that the social transfer of pain alters bystander peripheral physiology. These results are the first evidence of the potential for such a link.

microbiology↗

bioRxiv2025

Longitudinal changes in gut microbiota across reproductive states in wild baboons

BackgroundIn humans and other mammals, female reproduction is linked to extensive changes in physiology, immunity, hormones, and behavior. These changes likely shape, and may be shaped by, the composition of gut microbial communities. Characterizing the dynamics of gut microbial change across reproductive states, including its relationship to female physiology, is important for understanding how the gut microbiota influences female and offspring health. ResultsHere we characterize longitudinal changes in gut microbiota across reproduction by combining 16S rRNA gene sequencing data from 4,462 stool samples (spanning 14 years of sample collection) with life history data on multiple reproductive events in 169 female baboons. These baboons were members of a well-studied, natural baboon population in Kenya where reproductive state (ovarian cycling, pregnancy, and postpartum amenorrhea) is tracked daily and microbiota data could be paired with measurements of fecal-derived estrogen, progesterone, and glucocorticoid levels. We found extensive changes in baboon gut microbiota as females transitioned between reproductive states. Pregnancy was linked to distinct patterns of ASV richness, community composition, and taxonomic abundances compared to postpartum amenorrhea and ovarian cycling. The most dramatic shifts occurred as females transitioned from the first to second trimester of pregnancy, with altered abundances of taxa that have been linked, in humans and model systems, to host immunity, weight gain, or hormone levels. Host identity was consistently the strongest predictor of gut microbiota composition across states, and this individual signature was strongest during pregnancy. Estrogen and progesterone levels had robust associations with the gut microbiota overall, but the microbial taxa involved in these associations were reproductive state-dependent. Glucocorticoid concentrations were not a major predictor of gut microbiota composition in any state. ConclusionsTogether, our results support the idea that gut microbiota contribute to the complex physiological changes necessary during pregnancy, but that microbial changes during pregnancy are somewhat unique to each female. Variation in steroid hormones is associated with some, but not all, of these relationships, emphasizing the importance of considering steroid hormone levels in studies of gut microbiota variation. Our results motivate future work on how gut microbiota contribute to reproductive outcomes, including both maternal and offspring health.

evolutionary biology↗

bioRxiv2025

Spatiotemporal Microbial Ecoevolutionary Dynamics on the International Space Station

This study presents the most comprehensive spatiotemporal analysis of the ISS microbiome to date. Over a seven-year period, 184 surface samples were collected for live/dead metagenomic profiling, phenotypic characterization of antimicrobial resistance (AMR) and virulence among 102 cultured isolates, and metagenome-assembled genome (MAG) analysis to evaluate evolutionary selection pressures. Despite ecological stability, comparative genomics revealed ongoing microevolution through lateral gene transfer and selection for traits (e.g., radiation resistance and biocide tolerance). Importantly, predictions of AMR and virulence frequently misaligned with experimental outcomes, underscoring the need for functional validation. This dataset highlights a stable core microbiome that persists across years, punctuated by localized adaptation and gene flow. The ISS microbiome exemplifies both ecological resilience and microevolutionary innovation that can inform risk management for long-duration spaceflight.

microbiology↗

bioRxiv2025

Utility of a quantitative approach to microbial dysbiosis using machine learning in an African American cohort with self-reported hair loss

ObjectiveHair loss is a common issue that affects a large proportion of the population, leading to lower self-confidence and quality of life. Microbial dysbiosis of the scalp has been shown to be associated with several different disorders leading to hair loss. Though several "microbiome friendly" cosmetic treatments are currently on the market, there is no agreement on the best technique for assessing dysbiosis leading to a lack of scientific rigor for quantifying the effective treatments. To help address this, the association between self-perceived hair loss and the scalp microbiome in an African-American cohort (n=36) was investigated. MethodsUsing a self-controlled design, swabs were collected from both "sparse" and "normal" scalp sites. The scalp microbiome was characterized via 16S rRNA gene sequencing and a dysbiosis score was calculated based on the proportion of all taxa within the samples. Further, we identified the taxa that contributed most to abnormal or dysbiotic hair sites using a machine learning random forest classifier and a negative binomial mixed effects model. ResultsThe dysbiosis index is sensitive to participants self-assessment of hair loss and interindividual variation. We found a core set of operational taxonomic units (OTUs) assigned to 7 genera that significantly contributed to increased scalp dysbiosis. ConclusionThis study demonstrates that self-perceived hair loss is associated with significant and measurable alterations in the scalp microbiome using, making the reported dysbiosis index a practical tool that may be used to assess microbiome changes following cosmetic or medical interventions for hair loss and other microbiome-associated disorders.

microbiology↗

bioRxiv2024

Social and environmental predictors of gut microbiome age in wild baboons

Mammalian gut microbiomes are highly dynamic communities that shape and are shaped by host aging, including age-related changes to host immunity, metabolism, and behavior. As such, gut microbial composition may provide valuable information on host biological age. Here we test this idea by creating a microbiome-based age predictor using 13,563 gut microbial profiles from 479 wild baboons collected over 14 years. The resulting "microbiome clock" predicts host chronological age. Deviations from the clocks predictions are linked to some demographic and socio-environmental factors that predict baboon health and survival: animals who appear old-for-age tend to be male, sampled in the dry season (for females), and have high social status (both sexes). However, an individuals "microbiome age" does not predict the attainment of developmental milestones or lifespan. Hence, in our host population, gut microbiome age largely reflects current, as opposed to past, social and environmental conditions, and does not predict the pace of host development or host mortality risk. We add to a growing understanding of how age is reflected in different host phenotypes and what forces modify biological age in primates.

evolutionary biology↗

bioRxiv2023

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by L. iners regardless of HPV status

IntroductionThe cervicovaginal microbiota is influenced by host physiology, immunology, lifestyle, and ethnicity. We hypothesized that there would be differences in the cervicovaginal microbiota among pregnant, non-pregnant and menopausal women living in Puerto Rico with and without Human Papillomavirus (HPV) infection and cervical cancer. We specifically wanted to determine if the microbiota associated with variation in cervical cytology. A total of 294 women comprised of reproductive-age non-pregnant (N=196), pregnant (N=37), and menopausal (N=61) women were enrolled. The cervicovaginal bacteria was characterized by 16S rRNA amplicon sequencing, the HPV were genotyped with SPF10-LiPA, and cervical cytology was quantified. High-risk HPV (HR-HPV, 67.3%) was prevalent, including genotypes not covered by the 9vt HPV vaccine. Cervical lesions (34%) were also common. The cervical microbiota was dominated by Lactobacillus iners. Pregnant women in the 2nd and 3rd trimesters had decreased diversity and a decreased abundance of microbes associated with bacterial vaginosis. Women in menopause had greater alpha diversity, a greater proportion of facultative and strictly anaerobic bacteria, and higher cervicovaginal pH than pre-menopausal women. Cervical lesions were associated with greater alpha diversity. However, no significant associations between the microbiota and HPV infection (HR or LR-HPV types) were found. The cervicovaginal microbiota women living in Puerto Rican were either dominated by L. iners or diverse microbial communities regardless of a womans physiological stage. We postulate that the microbiota and the high prevalence of HR-HPV, increase the risk of cervical lesions of women living in Puerto Rico.

microbiology↗

bioRxiv2023

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: The METS-Microbiome Study

The relationship between the gut microbiota, short chain fatty acid (SCFA) metabolism, and obesity remains unclear due to conflicting reports from studies with limited statistical power. Additionally, this association has rarely been explored in large scale diverse populations. Here, we investigated associations between fecal microbial composition, predicted metabolic potential, SCFA concentrations, and obesity in a large (N = 1,934) adult cohort of African-origin spanning the epidemiologic transition, from Ghana, South Africa, Jamaica, Seychelles, and the United States (US). The greatest gut microbiota diversity and total fecal SCFA concentration was found in the Ghanaian population, while the lowest levels were found in the US population, respectively representing the lowest and the highest end of the epidemiologic transition spectrum. Country-specific bacterial taxa and predicted-functional pathways were observed, including an increased prevalence of Prevotella, Butyrivibrio, Weisella and Romboutsia in Ghana and South Africa, while Bacteroides and Parabacteroides were enriched in Jamaican and the US populations. Importantly, VANISH taxa, including Butyricicoccus and Succinivibrio, were significantly enriched in the Ghanaian cohort, reflecting the participants traditional lifestyles. Obesity was significantly associated with lower SCFA concentrations, a decrease in microbial richness, and dissimilarities in community composition, and reduction in the proportion of SCFA synthesizing bacteria including Oscillospira, Christensenella, Eubacterium, Alistipes, Clostridium and Odoribacter. Further, the predicted proportions of genes in the lipopolysaccharide (LPS) synthesis pathway were enriched in obese individuals, while genes associated with butyrate synthesis via the dominant pyruvate pathway were significantly reduced in obese individuals. Using machine learning, we identified features predictive of metabolic state and country of origin. Country of origin could accurately be predicted by the fecal microbiota (AUC = 0.97), whereas obesity could not be predicted as accurately (AUC = 0.65). Participant sex (AUC = 0.75), diabetes status (AUC = 0.63), hypertensive status (AUC = 0.65), and glucose status (AUC = 0.66) could all be predicted with different success. Interestingly, within country, the predictive accuracy of the microbiota for obesity was inversely correlated to the epidemiological transition, being greatest in Ghana (AUC = 0.57). Collectively, our findings reveal profound variation in the gut microbiota, inferred functional pathways, and SCFA synthesis as a function of country of origin. While obesity could be predicted accurately from the microbiota, the variation in accuracy in parallel with the epidemiological transition suggests that differences in the microbiota between obesity and non-obesity may be larger in low-to-middle countries compared to high-income countries. Further examination of independent study populations using multi-omic approaches will be necessary to determine the factors that drive this association.

microbiology↗

bioRxiv2022

Host and Water Microbiota are Differentially Linked to Potential Human Pathogen Accumulation in Oysters

Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. For example, bacterial pathogens from both marine and terrestrial sources concentrate in oysters and can cause human illness when oysters are consumed raw. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to oyster hosts and the microbial ecology of pathogenic bacteria likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of fecal indicators, Vibrio parahaemolyticus, and Vibrio vulnificus. Site-specific environmental conditions significantly influenced the composition and diversity of water microbial communities, which were linked to the highest concentrations of both Vibrio spp. and fecal indicator bacteria. Oyster microbial communities, however, were less impacted by environmental variability and exhibited less variability in microbial community diversity and accumulation of target bacteria. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated potential pathogens in oysters, especially V. parahaemolyticus. This included an increase in cyanobacteria in both water and oyster digestive gland microbial communities, which could represent an environmental vector for Vibrio spp. transport and decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters.

microbiology↗

bioRxiv2022

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed. ImportanceThis study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends.

microbiology↗

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↗

bioRxiv2019

Manner of death and demographic effects on microbial community composition in organs of the human cadaver

The microbiome serves important functions in human health, and postmortem, the microbial signatures of colonized organ tissue could be useful in helping to predict the manner of death in cases where this information is not known. We surveyed the microbiota (16S rRNA V4 amplicon sequencing) of 265 organ tissue samples including liver, blood, brain, heart, prostate, spleen and uterus from cadavers in Italy, Finland and the United States with confirmed manners of death comprising either accidental death, natural death, homicide, and suicide. Geographic locality (i.e. nationality) had a strong effect on observed microbial composition. Differing PERMANOVA results between unweighted and weighted UniFrac (nearly inverse results) suggest that specific bacteria may be associated with ethnicity and age, but that these differences are negligible when taking into account the relative abundance of bacterial taxa; weighted UniFrac measures suggest that although taxonomic composition may not vary significantly between different manners of death, PMI, or BMI categories, the relative abundance of specific taxa vary significantly. Various tissues exhibit differential associations with bacteria, and prostate and uterus were substantially different compared to other organs. For example, in Italian cadavers, the bacteria MLE1-12 permeated nearly all tissues, except the prostate and uterus. We identified specific bacterial ASVs as biomarkers of either natural or accidental death and suicide, but not for homicide. While the manner of death may have an impact on microbial associations, further investigation under more controlled conditions will be needed to validate whether these associations are predictive in forensic determinations.\n\nImportanceThe utilization of microbial data in the context of forensic investigations holds great promise for the field of forensic science. Identification of taxa that are associated with postmortem interval (PMI), specific manners of death (MOD), or other traits such as age, sex, ethnicity, and nationality may allow investigators to refine the circumstantial details surrounding the death of an individual. In this study we find nationality (geographic location of cadaver) to be a dominant predictor of cadaver microbiome composition. We also identify a number of cadaver-specific traits to be associated with microbial alpha- and beta diversity, as well as bacterial taxa that are differentially associated with these traits.

microbiology↗

bioRxiv2019

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures

The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering, and found that Minimum Entropy Decomposition (MED) was best able to distinguish between the microbial signatures of different individuals, and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand or shoe associated samples. For hand-associated samples, connection between cliques was enriched for hands, implicating them as a primary means of transmission. By contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with other individuals, while all floor and shoe samples consistently clustered together.\n\nImportanceHumans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the microbial signatures they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures, and how best to process sequencing data to best tease apart these signatures.

ecology↗

bioRxiv2019

The human microbiota is associated with cardiometabolic risk across the epidemiologic transition

Oral and fecal microbial biomarkers have previously been associated with cardiometabolic (CM) risk, however, no comprehensive attempt has been made to explore this association in minority populations or across different geographic regions. We characterized gut- and oral-associated microbiota and CM risk in 655 participants of African-origin, aged 25-45, from Ghana, South Africa, Jamaica, and the United States (US). CM risk was classified using the CM risk cut-points for elevated waist circumference, elevated blood pressure and elevated fasted blood glucose, low high-density lipoprotein (HDL), and elevated triglycerides. Gut-associated bacterial alpha diversity negatively correlated with elevated blood pressure and elevated fasted blood glucose. Similarly, gut bacterial beta diversity was also significantly differentiated by waist circumference, blood pressure, triglyceridemia and HDL-cholesterolemia. Notably, differences in inter- and intra-personal gut microbial diversity were geographic-region specific. Participants meeting the cut-points for 3 out of the 5 CM risk factors were significantly more enriched with Lachnospiraceae, and were significantly depleted of Clostridiaceae, Peptostreptococcaceae, and Prevotella. The predicted relative proportions of the genes involved in the pathways for lipopolysaccharides (LPS) and butyrate synthesis were also significantly differentiated by the CM risk phenotype, whereby genes involved in the butyrate synthesis via lysine, glutarate and 4-aminobutyrate/succinate pathways and LPS synthesis pathway were enriched in participants with greater CM risk. Furthermore, inter-individual oral microbiota diversity was also significantly associated with the CM risk factors, and oral-associated Streptococcus, Prevotella, and Veillonella were enriched in participants with 3 out of the 5 CM risk factors. We demonstrate that in a diverse cohort of African-origin adults, CM risk is significantly associated with reduced microbial diversity, and the enrichment of specific bacterial taxa and predicted functional traits in both gut and oral environments. As well as providing new insights into the associations between the gut and oral microbiota and CM risk, this study also highlights the potential for novel therapeutic discoveries which target the oral and gut microbiota in CM risk.

microbiology↗

bioRxiv2019

Quantifying and understanding well-to-well contamination in microbiome research

Microbial sequences inferred as belonging to one sample may not have originated from that sample. Such contamination may arise from laboratory or reagent sources or from physical exchange between samples. This study seeks to rigorously assess the behavior of this often-neglected between-sample contamination. Using unique bacteria each assigned a particular well in a plate, we assess the frequency at which sequences from each source appears in other wells. We evaluate the effects of different DNA extraction methods performed in two labs using a consistent plate layout including blanks, low biomass, and high biomass samples. Well-to-well contamination occurred primarily during DNA extraction, and to a lesser extent in library preparation, while barcode leakage was negligible. Labs differed in the levels of contamination. DNA extraction methods differed in their occurrences and levels of well-to-well contamination, with robotic methods having more well-to-well contamination while manual methods having higher background contaminants. Well-to-well contamination was observed to occur primarily in neighboring samples, with rare events up to 10 wells apart. The effect of well-to-well was greatest in samples with lower biomass, and negatively impacted metrics of alpha and beta diversity. Our work emphasizes that sample contamination is a combination of crosstalk from nearby wells and background contaminants. To reduce well-to-well effects, samples should be randomized across plates, and samples of similar biomass processed together. Researchers should evaluate well-to-well contamination in study design and avoid removal of taxa or OTUs appearing in negative controls, as many will be microbes from other samples rather than reagent contaminants.\n\nImportanceMicrobiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements including use of controls for validating accurate portrayals of microbial communities. In this study, we describe a previously undocumented form of contamination, well-to-well contamination and show that contamination primarily occurs during DNA extraction rather than PCR, is highest in plate-based methods as compared to single tube extraction, and occurs in higher frequency in low biomass samples. This finding has profound importance on the field as many current techniques to decontaminate a dataset simply relies on an assumption that microbial reads found in blanks are contaminants from outside namely the reagents or consumables.

genomics↗