Biology subjects

Lee, S. T. M.

Publications and source records attributed to Lee, S. T. M..

At least 19 recordsLinked to original sources

bioRxiv2025

Plant host identity drives Andropogon gerardii rhizobiome assembly strategies under increasing abiotic stress

Predicted changes in precipitation threaten tallgrass prairies by altering the soil microbial communities that are essential for plant resilience. Andropogon gerardii, a dominant grass in tallgrass prairies, spans the contiguous North American precipitation gradient. However, it remains unclear to what extent the rhizosphere microbiomes (rhizobiomes) are influenced by the plant-host environmental interaction. To assess how environmental and host factors shape the rhizobiome, we surveyed A. gerardii populations across 25 remnant prairie sites (June-August 2023) within its native range in the United States, characterizing the microbiomes in the rhizosphere and soils using 16S amplicon sequencing. We demonstrated that while geographic location largely structured both rhizosphere and soil communities, regional precipitation (60-day rainfall) emerged as a primary driver of the microbial community assembly. We observed distinct microbial divides across the dry and wet regions of the North American "arid-humid divide." Importantly, we found the first compelling large-scale evidence that regional precipitation has a profound influence on rhizobiome assembly. In the most arid regions, rhizosphere microbial communities exhibited significantly more predicted stochasticity than those in the local soil and contained taxa related to host-benefiting functions. Our study suggests that intensified host-driven selection for specific microbial variants occurs under heightened abiotic stress, highlighting the hosts pivotal role in shaping its rhizobiome composition in challenging environments.

microbiology↗

bioRxiv2025

Interactions Between Native Soil Microbiome and a Synthetic Microbial Community Reveals Bacteria with Persistent Traits

Synthetic microbial communities (SynComs) are curated microbial groups designed to enhance plant growth or disease resistance by augmenting soil microbiomes. Attaining SynCom stability in the presence of native soil communities remains a key challenge. This study investigated the survival, persistence, and chemical interactions of a SynCom with a native soil microbial community using a transwell system that spatially constrains bacteria while permitting chemical interactions. The SynCom, composed of six compatible Pseudomonas species identified through whole-genome sequencing, was analyzed for antagonistic interactions with native microbes over time and assessed using biomass and viability measurements. Over time, the SynCom exhibitedreduced growth in the presence of native soil microbes compared to the SynCom not exposed to the native microbes. Flow cytometry analysis showed an 81% reduction of live cells for the persistent strain in the presence of native microbes and a 78% and 99% increase in dead and unstained cells, respectively. Compared to a non-persistent strain, one persistent SynCom strain showed lower metabolic utilization across five key compound classes: polymers, carboxylic acids, amino acids, amines, and phenols when exposed to the native soil microbes. These findings underscore the importance of understanding complex SynCom-environment interactions to enhance SynCom stability and optimize in situ applications. ImportanceSynthetic Microbial Communities, or SynComs, are an emerging technology that can potentially augment plant health. Still, their application in situ depends on deciphering the complex interactions between SynCom microbes and native microbial communities. This study provides insight into several Pseudomonas strains displaying persistent characteristics, which makes these bacteria promising candidates for SynCom stability in implanted environments. Understanding the persistent traits of these bacteria is a vital advancement in SynCom technology, and an important next step toward implementing SynComs in agricultural systems.

microbiology↗

bioRxiv2024

Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance

BackgroundPlants evolved alongside microbes, enabling plants to better cope with abiotic and biotic stresses. The interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants have a "home field advantage" in recruiting microbes unique in their home environment, reflecting mutual recognition and the targeted recruitment of microbes. ResultsUsing gene- and genome-centric approaches, we assessed the functional potential of root-associated microbes and profiled the host metabolites to uncover the metabolic outputs potentially regulating host-microbe interactions. Our results showed that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine was highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses. ConclusionThis study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance hosts ability to thrive in a stressful environment. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture in the face of climate change.

microbiology↗

bioRxiv2024

Eubacterium rectale detoxification mechanism increases resilience of the gut environment

Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment. We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and ROS levels. Cell free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells. We demonstrated through an array of multi omics and molecular techniques that glutathione (GSH) biosynthesized by E. rectale was able to alleviate host ROS damage. We further showed downregulation of cell stress and immune response genes by host RNA sequencing, which is evidence that E. rectale microbial products promote recovery and alleviate ROS stress. HighlightsO_LILachnospiraceae detection correlated with lower host inflammation in vertically transmitted dysbiotic mice C_LIO_LICell free spent media from E. rectale lowered ROS and nitric oxide levels when introduced to stressed Caco-2 cells more effectively than 4 other strains of Lachnospiraceae C_LIO_LIEubacterium rectale spent media products include high levels of glutathione (GSH), carbohydrates, and amino acids C_LIO_LIEubacterium rectale potential gene function for glutathione biosynthesis and metabolism found in the genome C_LIO_LILower expression of repair and stress genes of intestinal cells treated with hydrogen peroxide was observed with E. rectale CFSM as well as treatment with 15 mM GSH C_LI

microbiology↗

bioRxiv2023

Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy

BackgroundGlobal change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. ResultsWe resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. ConclusionsThe outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.

bioinformatics↗

bioRxiv2023

Heat Tolerance is Affected by the Gut Microbiota in a Vertebrate Ectotherm

The gut microbiota is known to influence and have regulatory effects in diverse physiological functions of host animals, but only recently has the relationship between host thermal biology and gut microbiota been explored. Here, we examined how early-life manipulations of the gut microbiota in larval amphibians influenced their critical thermal maximum (CTmax) at different acclimation temperatures. We removed the resident microbiome on the outside of wild-caught wood frog (Lithobates sylvaticus) egg masses via an antibiotic wash, and then either maintained eggs without a microbiota or inoculated eggs with pond water or the intestinal microbiota of another species, green frogs (L. clamitans), that have a wider thermal tolerance. We predicted that this cross-species transplant would improve the CTmax of the recipient wood frog larvae relative to the other treatments. In line with this prediction, green frog-recipient larvae had the highest CTmax while those with no inoculum had the lowest CTmax. Both the microbiome treatment and acclimation temperature significantly influenced the larval gut microbiota communities and alpha diversity indices. Green frog inoculated larvae were enriched in Rikenellaceae relative to the other treatments, which produce short-chain fatty acids and could contribute to greater energy availability and enhanced heat tolerance. Larvae that received no inoculation had higher relative abundances of potentially pathogenic Aeromonas spp., which negatively affects host health and performance. Our results are the first to show that cross-species gut microbiota transplants alter heat tolerance in a predictive manner. This finding has repercussions for the conservation of species that are threatened by climate change and demonstrates a need to further explore the mechanisms by which the gut microbiota modulates host thermal tolerance.

zoology↗

bioRxiv2023

Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and rhizobiome

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict the species responses to environmental change. We used reciprocal gardens planted with distinct regional Andropogon gerardii ecotypes adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotype effect highlighted active microbial recruitment in the rhizosphere driven by ecotype or plant genetic background. Our data also suggest that ecotypes were more successful in recruiting rhizosphere community members unique to their local homesites, supporting the "home field advantage" hypothesis. These unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Further, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced effects of plant ecotypes on the rhizosphere microbiome recruitment. Our results should facilitate expanded studies on understanding the complexity of plant host interactions with local soil microbes and identification of functional potential of recruited microbes. Our study has the potential to aid in predicting ecosystem responses to climate change and the impact of management on restoration practices. ImportanceIn this study, we used reciprocal gardens located across a sharp precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional Andropogon gerardii ecotypes. We used16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though the location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site". We found evidence for "home field advantage" interactions between the host and associated rhizobiomes, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study provides insights into the understanding of factors effecting the plant adaptation, improving management strategies, and predicting of the future landscape under the changing climate.

microbiology↗

bioRxiv2022

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

BackgroundArchaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focussing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea detection and methanogenic functions while assessing global and host distribution of our novel archaeal metagenome assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, and MAG taxonomic assignment and functional annotation. ResultsWe generated 1,130 non-redundant MAGs with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in monogastric archaea which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further our understanding of microbiome development and functions.

microbiology↗

bioRxiv2022

High proportions of single-nucleotide variations associated with multidrug resistance in swine gut microbial populations

BackgroundAntimicrobial resistance (AMR) is a significant global public health concern associated with millions of deaths annually. Agriculture has been attributed as a leading factor in AMR and multidrug resistance (MDR) associated with swine production estimated as one of the largest agricultural consumers of antibiotics. Therefore, studying and understanding AMR in swine has global relevance. AMR research has received increased attention in recent years. However, we are still building our understanding of genetic variation within a complex gut microbiome system that impacts AMR and MDR. In order to evaluate the gut resistome, we evaluated genetic variation before, during, and after antibiotic treatments. We studied three treatment groups: non-antibiotic controls (C), chlortetracycline (CTC) treated, and tiamulin (TMU) treated. We collected fecal samples from each group and performed metagenomic sequencing for a longitudinal analysis of genetic variation and functions. ResultsWe generated 772,688,506 reads and 81 metagenome assembled genomes (MAGs). Interestingly, we identified a subset of 11 MAGs with sustained detection and high sustained entropy (SDHSE). Entropy described genetic variation throughout the MAG. Our SDHSE MAGs were considered MDR as they were identified prior to, throughout, and after CTC and TMU treatments as well as in the C piglets. SDHSE MAGs were especially concerning as they harbored relatively high variation. Consistently high variation indicated that these microbial populations may contain hypermutable elements which has been associated with increased chance of AMR and MDR acquisition. Our SDHSE MAGs demonstrated that MDR organisms (MDRO) are present in swine, and likely additional hosts contributing to global AMR. Altogether, our study provides comprehensive genetic support of MDR populations within the gut microbiome of swine.

microbiology↗

bioRxiv2022

Limitation of sulfur-containing amino acid availability by specific bacterial populations during enhanced colitis in IBD mouse model

Members of the Enterobacteriaceae family including Escherichia coli are associated with persistent gut inflammation during disorders like inflammatory bowel disease. This is due to rapid microbial colonization during dysbiosis combined with pathogenic tendencies. We characterized the dysbiotic gut community, defined potential functional pathways, and investigated crosstalk between host gene expression and microbial detections in an intestinal inflammation murine model. Members of Enterobacteriaceae family and the Enterococcus genus were highly detected in dysbiotic mice. These metagenome assembled genomes (MAGs) contained several virulence factors and metabolic pathways necessary to drive perpetual inflammation. Two Enterobacteriaceae MAGs with L-cysteine and L-taurine dioxygenases were strongly correlated with upregulation of the host gene CSAD, responsible for cysteine metabolism. Suggesting these bacteria compete with the host to utilize essential amino acids. We observed that bacterial isolates from dysbiotic mice displayed increased growth rates supplemented with L-cysteine, confirming that these microbes can utilize host nutrients to sustain inflammation. In BriefInflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species, however the mechanisms are unclear. Richie et al. show that these bacterial populations use sulfur metabolism and tolerate host-derived immune-response, to drive host inflammation and fuel growth in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize these essential host nutrients. HighlightsO_LIMice receiving native microbial FMT showed lower colon inflammation scores, higher microbial diversity, detections and gene expression similar to control mice. C_LIO_LIDysbiotic mice displayed increased colon inflammation, higher detection of potential pathogenic MAGs, and upregulation of cysteine dioxygenase and other inflammation response genes C_LIO_LIMAGs assigned to Enterococcus and Enterobacteriaceae species were more frequently detected in dysbiotic mice, while almost absent in mice receiving FMT or control mice, they also contain several virulence factors and antibiotic resistance genes. C_LIO_LIThese MAGs also display potential functions of utilizing host products and nutrients including nitrate, cysteine, and taurine to further fuel their growth and metabolism, which results in persistent host intestinal inflammation. C_LIO_LIIsolates in the Enterobacteriaceae family from dysbiotic mice utilize L-cysteine for growth, whereas isolates from FMT and control mice show no significant difference, indicating these bacteria can utilize the host derived cysteine. C_LI

genomics↗

bioRxiv2022

Culturomics of Andropogon gerardii rhizobiome revealed nitrogen transforming capabilities of stress-tolerant Pseudomonas under drought conditions

BackgroundClimate change will result in more frequent droughts that impact soil-inhabiting microbiomes in the agriculturally vital North American perennial grasslands. In this study, we used the combination of culturomics and high-resolution genomic sequencing of microbial consortia isolated from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. ResultsPhylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified the bacterial population of interest - MAG-Pseudomonas. Further metabolic pathway and pangenome analyses detected genes and pathways related to nitrogen transformation and stress responses in MAG-Pseudomonas. ConclusionsOur data indicate that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant hosts growth during stressful conditions. This study provided insights into optimizing plant productivity under drought conditions.

microbiology↗

bioRxiv2022

Stability and volatility shape the gut bacteriome and mycobiome dynamics in a pig model

The gut microbiome plays important roles in the maintenance of health and pathogenesis of diseases in the growing host. In order to fully comprehend the interplay of the gut microbiome and host, a foundational understanding of longitudinal bacteriome and mycobiome development is necessary. In this study, we evaluated enteric bacterial, fungal and host dynamics throughout the lifetime of commercial swine. We collected a total of 234 fecal samples from 9 pigs across 31 time points in 3 developmental stages (5 preweaning, 15 nursery, and 11 growth adult). We then performed 16S rRNA amplicon sequencing for bacterial profiles and qPCR for the fungus Kazachstania slooffiae. We identified distinct bacteriome clustering according to the host developmental stage, with the preweaning stage exhibiting low bacterial diversity and high volatility amongst samples. We further recovered clusters of bacterial populations that were considered core, transient and increasing throughout the host lifetime, suggesting distinct yet important roles by which these differing bacterial population clusters played in the different host stages. Kazachstania slooffiae was absent in the preweaning stage but peaked during the nursery stage of the host. We determined that all host growth stages contained negative correlations between K. slooffiae and bacterial genera, with only the growth adult stage containing positive correlates. The lack of positive correlates and shared K. slooffiae-bacteria interactions between stages warrants future research into the interactions amongst these kingdoms for host health. This research is foundational for understanding how the bacteriome and mycobiome develop singularly, as well as within a complex ecosystem in the hosts gut environment.

microbiology↗

bioRxiv2021

Bacteria but not fungi communities differ among perennial grassland ecotypic rhizosphere under abiotic environmental stress

Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of a dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species range in Colby Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after ten years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western KS as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after ten years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought.

bioinformatics↗

bioRxiv2021

D155Y Substitution of SARS-CoV-2 ORF3a Weakens Binding with Caveolin-1: An in silico Study

The clinical manifestation of the recent pandemic COVID-19, caused by the novel SARS-CoV-2 virus, varies from mild to severe respiratory illness. Although environmental, demographic and co-morbidity factors have an impact on the severity of the disease, contribution of the mutations in each of the viral genes towards the degree of severity needs a deeper understanding for designing a better therapeutic approach against COVID-19. Open Reading Frame-3a (ORF3a) protein has been found to be mutated at several positions. In this work, we have studied the effect of one of the most frequently occurring mutants, D155Y of ORF3a protein, found in Indian COVID-19 patients. Using computational simulations we demonstrated that the substitution at 155th changed the amino acids involved in salt bridge formation, hydrogen-bond occupancy, interactome clusters, and the stability of the protein compared with the other substitutions found in Indian patients. Protein-protein docking using HADDOCK analysis revealed that substitution D155Y weakened the binding affinity of ORF3a with caveolin-1 compared with the other substitutions, suggesting its importance in the overall stability of ORF3a-caveolin-1 complex, which may modulate the virulence property of SARS-CoV-2.

bioinformatics↗

bioRxiv2021

Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut

Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments, and reveal taxon-independent markers of dysbiosis that may explain why widespread yet typically low abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.

microbiology↗

bioRxiv2020

Detection of stress functional responses in bacterial populations under dry soil conditions show potential microbial mechanisms to resist drought conditions

Climate change is predicted to have a negative effect on the grasslands of the United States and will be detrimental to the economy and environment. The changing precipitation levels would also have an effect on the structural and functional potential of associated soil microbiome communities, which in turn will regulate the health of the plants during stressful conditions. In this study, we applied metagenomics analyses to capture the responses of the bacterial populations under drier soil conditions. We collected soil from two sites (dry and wet) at the Konza Long-Term Ecological Research field station in Kansas, which had characteristic features of the native prairies. Soil drying resulted in a significant shift in the bacterial population at the community level. Following that, fifteen bacterial genomes were short-listed based on the availability in the public database, higher relative abundance in dry soils than in wet, and also according to their contributions in drier soil. The potential microbial mechanisms were elucidated when an in-depth analysis of the functional genes was performed. Translation elongation factor EF-Tu, thiamine biosynthesis protein, and catalase were identified as a part of the overall stress functional responses in the bacterial population in this study. We speculate that these identified bacterial populations are important for maintaining the health of the soil under dry conditions. Genes and/or pathways found in this study provide insights into microbial mechanisms that these bacterial populations might employ to resist challenging drought conditions.

genomics↗

bioRxiv2020

Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model

Background & AimsInflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts. MethodsUsing the IL-10 gene-deficient (IL-10 KO) murine model where early life dysbiosis from antibiotic (cefoperozone, CPZ) treated dams vertically-transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to eventual clinical outcomes. ResultsCompared to controls, offspring acquiring maternal CPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership both in bacteriome and mycobiome that were associated with alterations in specific functional subsystems. Furthermore, among IL-10 KO offspring from CPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome. ConclusionsOur findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD. SynopsisCurrently, predictive markers for the development and course of inflammatory bowel diseases (IBD) are not available. This study supports the notion that gut microbiome metagenomic profiles could be developed into a useful tool to assess risk and manage human IBD.

microbiology↗

bioRxiv2020

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis

Perturbations in the early life gut microbiome are associated with increased risk to complex immune disorder like inflammatory bowel diseases. We previously showed maternal antibiotic-induced gut dysbiosis vertically passed to offspring increases experimental colitis risk in IL-10 gene deficient (IL-10-/-) mice. While this could arise from emergence of pathobionts or loss/lack of essential microbes needed for appropriate immunological education, our findings suggest the latter. A dominant Bacteroides strain absent following antibiotic-induced perturbation was cultivated from murine fecal samples. Addition of this strain into mice with antibiotic-induced dysbiosis significantly promoted immune tolerance and reduced incidence of colitis in IL-10-/- mice, but only if engrafted early in life, and not during adulthood. Thus, key members of the gut microbiome are essential for development of immune tolerance to commensal microbes in early life and their addition in presence of gut dysbiosis during this period can reduce colitis risk in genetically prone hosts. HighlightsO_LISpecific gut microbes promote early life immune tolerance to key commensal microbes C_LIO_LILoss of early life keystone microbes increases colitis risk in genetically prone hosts C_LIO_LIEmergence of absent commensal microbes late in life worsened colitis outcome C_LIO_LIEarly life exposure to a missing keystone Bacteroides strain reduced colitis risk C_LI

microbiology↗