bluuebunny/crossref_metadata_2025 huggingface dataset:
Not all stool is created equal: Strain engraftment competition and functional augmentation in a multi-donor faecal microbiota transplantation trial for obesity
Authors: Wilson Brooke
Published: September 2024

Transplantation of faecal microbiota (FMT) from healthy lean donors has been shown to transiently improve insulin sensitivity and alter fat distribution in individuals with obesity and metabolic syndrome. However, the mechanisms and levels of donor strain engraftment required to elicit these effects remain poorly characterised. To address this, we performed a double-blinded randomised placebo-controlled trial for FMT in 87 adolescents with obesity. Participants were randomized to receive multi-donor FMT (capsules containing the fecal microbiota of four healthy, lean, sex-matched donors) or placebo (saline capsules). Following a bowel cleanse, participants ingested a total of 28 capsules over two consecutive days. FMT capsules and recipient stool samples collected at baseline, 6-, 12- and 26-weeks post-treatment were analysed by shotgun metagenomic sequencing allowing us to track donor strain engraftment and monitor changes in the recipient gut microbiome over time. We found that multi-donor FMT sustainably altered the structure and functional potential of the gut microbiome for up to six months. In what was effectively a microbiome competition experiment, we discovered that two donor microbiomes (one female, one male) dominated strain engraftment. These ‘super-donor’ microbiomes were characterized by high microbial diversity and a high Prevotella to Bacteroides ratio. Engrafted strains led to enterotype-level shifts in community composition and provided genes that altered the metabolic potential of the microbiome, including pathways previously shown to be important in energy balance homeostasis (e.g. NAD biosynthesis). Despite our attempts to standardize FMT dose and donors, FMT recipients varied widely in their engraftment of donor strains suggesting the host environment plays a critical role in mediating FMT receptivity. Further work is required to better understand the various host-microbe interactions that determine engraftment success to help in developing more effective and personalised microbial therapies.

Link to OA paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01060-7
Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease
Authors: Hoskinson Courtney
Published: September 2024

Allergic diseases affect millions of people worldwide. An increase in their prevalence has been associated with alterations in the gut microbiome, i.e., the microorganisms and their genes within the gastrointestinal tract. Maturation of the infant immune system and gut microbiota occur in parallel; thus, the conformation of the microbiome may determine if tolerant immune pro- gramming arises within the infant. Here we show, using deeply phenotyped participants in the CHILD birth cohort (n = 1115), that there are early-life influences and microbiome features which are uniformly associated with four distinct allergic diagnoses at 5 years: atopic dermatitis (AD, n = 367), asthma (As, n = 165), food allergy (FA, n = 136), and allergic rhinitis (AR, n = 187). In a subset with shotgun metagenomic and metabolomic profiling (n = 589), we discover that impaired 1-year microbiota maturation may be universal to pediatric allergies (AD p = 0.000014; As p = 0.0073; FA p = 0.00083; and AR p = 0.0021). Extending this, we find a core set of functional and metabolic imbalances characterized by compromised mucous integrity, elevated oxida- tive activity, decreased secondary fermentation, and elevated trace amines, to be a significant mediator between microbiota maturation at age 1 year and allergic diagnoses at age 5 years (βindirect = −2.28; p = 0.0020). Microbiota maturation thus provides a focal point to identify deviations from normative development to predict and prevent allergic disease.

Link to publication (OA): https://www.nature.com/articles/s41467-023-40336-4
Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome
Authors: Huang Xinyu
Published: September 2024

Background: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 meters below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown, especially identifying the genetic mobility of resistance and pathogenicity in unculturable trench bacteria is a great challenge. This study aims to depict the landscape of virulome, antibiotic resistome and mobilome of the hadal zone microbiota of the Mariana Trench.

Method: The landscape of virulence and antibiotic resistance genes was depicted based on high-throughput metagenomic sequencing analysis using both sequence-based and domain-based annotation methods. The mobility and spread potentials of ARGs and virulence genes via horizontal gene transfer (HGT) were examined by checking their co-occurrence with MGEs.

Results and Discussion: i) the Challenger Deep bottom (10,898-m) sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance (Fig. 1b and 2b), compared with the other Marian Trench sediment; ii) both the abundance and richness of ARGs greatly differed across sediment sites in the following increasing trend: SM10898 - SM6038 - SP5856 (Fig. 2a). Surprisingly, the bottom site of the Challenger Deep was found to still harbor 20 subtypes of known ARGs. Both the abundance (1.08 to 1.12×10-1 GP16S each) and diversity (127 to 153 subtypes) of the hadal seawater ARGs (Fig. 2b) were surprisingly high in the hadal seawater of the Mariana trench. The abundance of ARGs in seawater is higher than that in sediments by up to two orders of magnitude, deterministic natural processes drivers the resistome differences between hadal sediment and seawater including habitat (environmental) filtering and biotic interactions (e.g., competition). iii) HGT mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria (Fig. 3a); iv) substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria (Fig. 4).
Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota
Authors: Gill Tejpal
Published: September 2024

Objective To investigate whether axial spondyloarthritis (AxSpA) patients have an altered immunoglobulin A (IgA) response in the gut and oral microbial communities. Methods We performed 16S rRNA gene (16S) sequencing on IgA positive (IgA+) and IgA negative (IgA−) fractions (IgA-SEQ) from feces (n=17 AxSpA; n=14 healthy) and saliva (n=17 AxSpA; n=12 healthy), as well as on IgA-unsorted fecal and salivary samples. PICRUSt2 was used to predict microbial metabolic potential in AxSpA patients and healthy controls (HCs). Results IgA-SEQ revealed enrichment of several microbes in the fecal (Akkermansia, Ruminococcaceae, Lachnospira) and salivary (Prevotellaceae, Actinobacillus) microbiome in AxSpA patients as compared with HCs. Fecal microbiome from AxSpA patients showed a trend towards increased alpha diversity of the IgA+ fraction and decreased diversity in the IgA− fraction in comparison with HCs, while the salivary microbiome exhibits a significant decrease in alpha diversity in both IgA+ and IgA− fractions. Increased IgA coating of Clostridiales Family XIII correlated with disease severity. Inferred metagenomic analysis suggests perturbation of metabolites and metabolic pathways for inflammation (oxidative phosphorylation, glutathione metabolism) and metabolism (propanoate and butanoate metabolism) in AxSpA patients. Conclusions Analyses of fecal and salivary microbes from AxSpA patients reveal distinct populations of immunoreactive microbes using novel IgA-SEQ approach, which were not captured by comparing their relative abundance with HCs. Predictive metagenomic analysis revealed perturbation of metabolites/metabolic pathways in AxSpA patients. Future studies on these immunoreactive microbes may lead to better understanding of the functional role of IgA in maintaining microbial structure and human health.
Critical Assessment of Metagenome Interpretation - the second round of challenges
Authors: McHardy Alice
Published: September 2024

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from ∼1,700 novel and known microbial genomes, as well as ∼600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results.

Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.
Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices
Authors: Huang Kun D.
Published: September 2024

The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.

Link to publication: https://www.sciencedirect.com/science/article/pii/S2666379124000491
Discovery and Characterisation of Temperate Gut Bacteriophages
Authors: Barr Jeremy
Published: September 2024

Bacteriophages are ubiquitous across all environments and influence their bacterial hosts in diverse ways. Within the human gut the bacterial concentration is estimated to be around 1011 cells per gram of faeces, yet the phage concentration is significantly lower at around 109 phages per gram of faeces. However, these raw counts fail to capture the prophages, which are integrated phages residing withing a bacterial host chromosome. Prophages can constitute up to 20% of the host bacterial genome, greatly impacting their host’s function, evolution, and diversification. Here we characterised a large collection of bacterial isolates originating from the human gut and identify their prophage elements. Using a broad panel of induction conditions under anaerobic conditions we identify and begin to experimentally characterise these novel and actively replicating temperate phages of the human gut.
Software testing in microbial bioinformatics: a call to action
Authors: Mendes Inês
Published: September 2024

Computational algorithms have become an essential component of microbiome research, with great efforts by the scientific community to raise standards on the development and distribution of code. Despite these efforts, sustainability and reproducibility are major issues since continued validation through software testing is still not a widely adopted practice. In the field of microbial bioinformatics, good software engineering practices are not yet widely adopted. Many microbial bioinformaticians start out as (micro)biologists and subsequently learn how to code. Without abundant formal training, a lot of education about good software engineering practices comes down to an exchange of information within the microbial bioinformatics community. Here, we report seven recommendations that help researchers implement software testing in microbial bioinformatics. These recommendations are: Establish software needs and testing goals; Use appropriate input test files; Use an easy-to-follow language format to implement testing; Try to automate testing; Test across multiple computational setups; and Encourage others to test your software. We propose collaborative software testing as an opportunity to continuously engage software users, developers, and students to unify scientific work across domains. As automated software testing remains underused in scientific software, our set of recommendations not only ensures appropriate effort can be invested into producing high quality and robust software but also increases engagement in its sustainability. We have developed these recommendations based on our experience from a collaborative hackathon organised prior to the American Society for Microbiology Next Generation Sequencing (ASM NGS) 2020 conference. We also present a repository hosting examples and guidelines for testing, available from https://github.com/microbinfie-hackathon2020/CSIS.

Link to OA paper: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000790
Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
Authors: Quinn-Bohmann Nick
Published: September 2024

Microbially-derived short-chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation, and integrity of the intestinal epithelium. However, the production of SCFAs can vary widely between individuals consuming the same diet, with lower levels often associated with disease. A mechanistic understanding of this heterogeneity is lacking. We present a microbial community-scale metabolic modeling (MCMM) approach to predict individual-specific SCFA production profiles. We assess the quantitative accuracy of our MCMMs using in vitro, ex vivo, and in vivo data. Next, we identify associations between MCMM SCFA predictions and a panel of blood-based clinical chemistries in a large human cohort. Finally, we demonstrate how MCMMs can be leveraged to design personalized dietary, prebiotic, and probiotic interventions that optimize SCFA production in the gut. Our results represent an important advance in engineering gut microbiome functional outputs for precision health and nutrition.
Microbiome and Women's Health
Authors: Manara Serena
Published: September 2024

Panel discussion of the Microbiome and Women's Health event
Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome
Authors: Kindschuh William F.
Published: September 2024

Spontaneous preterm birth (sPTB) is a leading cause of maternal and neonatal morbidity and mortality, yet its prevention and early risk stratification are limited. Previous investigations have suggested that vaginal microbes and metabolites may be implicated in sPTB. Here we performed untargeted metabolomics on 232 second-trimester vaginal samples, 80 from pregnancies ending preterm. We find multiple associations between vaginal metabolites and subsequent preterm birth, and propose that several of these metabolites, including diethanolamine and ethyl glucoside, are exogenous. We observe associations between the metabolome and microbiome profiles previously obtained using 16S ribosomal RNA amplicon sequencing, including correlations between bacteria considered suboptimal, such as Gardnerella vaginalis, and metabolites enriched in term pregnancies, such as tyramine. We investigate these associations using metabolic models. We use machine learning models to predict sPTB risk from metabolite levels, weeks to months before birth, with good accuracy (area under receiver operating characteristic curve of 0.78). These models, which we validate using two external cohorts, are more accurate than microbiome-based and maternal covariates-based models (area under receiver operating characteristic curve of 0.55–0.59). Our results demonstrate the potential of vaginal metabolites as early biomarkers of sPTB and highlight exogenous exposures as potential risk factors for prematurity.

Link to paper: https://www.nature.com/articles/s41564-022-01293-8
Adaptation of Anaerobic Digestion Microbial Communities to High Ammonium Levels: Insights from Strain-Resolved Metagenomics
Authors: Ghiotto Gabriele
Published: September 2024

In anaerobic digestion (AD), a complex microbial community orchestrates the conversion of organic carbon into CO2 and CH4, with anaerobic archaea playing a pivotal role in methanogenesis. However, AD efficiency can be compromised by various factors, including temperature, pH, O2, salt, and ammonia concentration, with ammonia being a major culprit. Ammonia inhibition often arises when processing N-rich organic wastes, leading to potential disruptions in the digestion process. The toxicity of ammonia in AD is governed by its forms, ammonia and ammonium (NH4+), which are in equilibrium based on temperature and pH. Ammonia toxicity imposes challenges by disrupting intracellular pH and demanding additional energy. Free ammonia nitrogen can penetrate cells, interfering with essential cations and affecting metabolic reactions. Accumulated NH4+ can further destabilize intracellular pH and disrupt cation dynamics. Microbes exposed to toxic ammonia may undergo random mutations that confer a survival advantage. These adaptive mutations enable microbes to enhance their tolerance to ammonia toxicity, modifying proteins involved in stress responses. In this study, a stepwise increase in ammonia concentration up to 20 g NH4+-N/L was explored, a range not previously investigated. Genomic heterogeneity within the AD microbiome and the role of variants have received limited attention in prior research. The study introduced an innovative approach, utilizing strain-resolved metagenomics and single nucleotide variants (SNVs) to monitor microbial dynamics. This approach allowed for a comparative analysis of genetic and ecological fluctuations at both species and strain levels in response to ammonia stress. The study aimed to understand the extent to which microbial communities could adapt to ammonia stress and uncover ammonia-tolerant methanogenic consortia. The results unveiled fine-scale evolutionary mechanisms, functional dynamics, and metabolic variations within the microbial community. Specifically, the archaeon Methanoculleus bourgensis vb3066 and the putative syntrophic acetate-oxidizing bacterium Acetomicrobium sp. ma133 accumulated through generations positively selected SNVs within genes associated with stress adaptation. Additionally, the study highlighted the presence of multiple coexisting strains within species, indicating an additional layer of diversity beyond the species level. In summary, this study delves into the challenges posed by ammonia inhibition in anaerobic digestion processes. By employing advanced techniques in metagenomics and SNV analysis, it provides a comprehensive understanding of how microbial communities adapt to ammonia stress and offers insights into the selection of ammonia-tolerant microorganisms.
Processed foods drive intestinal barrier permeability and microvascular diseases
Authors: Snelson Matthew
Published: September 2024

Intake of processed foods has increased markedly over the past decades, coinciding with increased microvascular diseases such as chronic kidney disease (CKD) and diabetes. Here, we show in rodent models that long-term consumption of a processed diet drives intestinal barrier permeability and an increased risk of CKD. Inhibition of the advanced glycation pathway, which generates Maillard reaction products within foods upon thermal processing, reversed kidney injury. Consequently, a processed diet leads to innate immune complement activation and local kidney inflammation and injury via the potent proinflammatory effector molecule complement 5a (C5a). In a mouse model of diabetes, a high resistant starch fiber diet maintained gut barrier integrity and decreased severity of kidney injury via suppression of complement. These results demonstrate mechanisms by which processed foods cause inflammation that leads to chronic disease.

Link to OA paper: https://www.science.org/doi/10.1126/sciadv.abe4841
Microbiota links to neural dynamics supporting threat processing
Authors: Hall Caitlin
Published: September 2024

There is growing recognition that the composition of the gut microbiota influences behaviour, including responses to threat. The cognitive-interoceptive appraisal of threat-related stimuli relies on dynamic neural computations between the anterior insular (AIC) and the dorsal anterior cingulate (dACC) cortices. If, to what extent, and how microbial consortia influence the activity of this cortical threat processing circuitry is unclear. We addressed this question by combining a threat processing task, neuroimaging, 16S rRNA profiling, and computational modelling in healthy participants. Results showed interactions between high-level ecological indices with threat-related AIC-dACC neural dynamics. At finer taxonomic resolutions, the abundance of Ruminococcus was differentially linked to connectivity between, and activity within the AIC and dACC during threat updating. Functional inference analysis provides a strong rationale to motivate future investigations of microbiota-derived metabolites in the observed relationship with threat-related brain processes.
Characterizing microbial community viability with RNA-based high-throughput sequencing
Authors: Wang Ya Lea
Published: September 2024

Characterization of microbial community viability is of great importance: essentially all sequence-based technologies do not differentiate living from dead microbes, whereas the functions and phenotypes of microbial communities are defined by biochemically active (“viable”) organisms. As a result, our understanding of microbial community structures and their potential transmission mechanisms remains incomplete. As a potential solution to this issue, 16S RNA-based amplicon sequencing (not rRNA gene, but the rRNA transcripts) has been proposed as a method to quantify the viable fraction of a microbial community, but its reliability has not been evaluated systematically. Here, we present our work to benchmark 16S-RNA-seq (targeting 16S rRNA transcripts and genes for parallel RNA and DNA sequencing) for viability assessment in synthetic and realistic microbial communities. In synthetic communities, we found that 16S-RNA-seq successfully reconstructed the mixtures of heat-killed Escherichia coli and Streptococcus sanguinis. We then applied this technique to natural communities (computer screens and mice, soil, and saliva) spiked with known concentrations of living and heat-killed E. coli to evaluate its performance in realistic conditions. No significant compositional differences were explained by the 16S-RNA assessment, suggesting that 16S-RNA-seq is not appropriate for viability assessment in complex communities. Results were slightly different when evaluated in environmental samples of similar origins (i.e. from Boston subway systems), samples were differentiated both by environments as well as by library type. Overall, these results show that 16S-RNA-seq has promise, but that previous literature assuming that 16S-rRNA amplicons are directly, quantitatively enriched for viable microbes is likely incorrect, as the technique does not reflect microbial viability outside of very simple, synthetic “communities.” We are currently continuing this work to develop new RNA amplicon-seq markers based on protein-encoding genes cpn60, as well as to improve viability assessment with multi-omic integration, e.g. combining amplicon-seq with functional indicators such as metatranscriptomic and metaproteomic profiles. These can circumvent some of the current limitations of 16S-RNA-seq, providing a complementary definition of viability, and directly observing activities such as virulence, pathogenicity, or antimicrobial resistance that are not captured by amplicon sequencing.
Effective binning of metagenomic contigs using contrastive multi-view representation learning
Authors: Wang Ziye
Published: September 2024

Contig binning plays a crucial role in metagenomic data analysis by grouping contigs from the same or closely related genomes. However, existing binning methods face challenges in practical applications due to the diversity of data types and the difficulties in efficiently integrating heterogeneous information. Here, we introduce COMEBin, a binning method based on contrastive multi-view representation learning. COMEBin utilizes data augmentation to generate multiple fragments (views) of each contig and obtains high-quality embeddings of heterogeneous features (sequence coverage and k-mer distribution) through contrastive learning. Experimental results on multiple simulated and real datasets demonstrate that COMEBin outperforms state-of-the-art binning methods, particularly in recovering near-complete genomes from real environmental samples. COMEBin outperforms other binning methods remarkably when integrated into metagenomic analysis pipelines, including the recovery of potentially pathogenic antibiotic-resistant bacteria (PARB) and moderate or higher quality bins containing potential biosynthetic gene clusters (BGCs).

Link to OA paper: https://www.nature.com/articles/s41467-023-44290-z
Wastewater sequencing reveals community and variant dynamics of the collective human virome
Authors: Tisza Mike
Published: September 2024

Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.

Link to OA paper: https://www.nature.com/articles/s41467-023-42064-1
Cas9-Assisted Biological Containment of a Genetically Engineered Human Commensal Bacterium and Genetic Elements
Authors: Hayashi Naoki
Published: September 2024

Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.

Link to OA paper: https://www.nature.com/articles/s41467-024-45893-w
Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications
Authors: Agostinetto Giulia
Published: September 2024

Boosted by the exponential growth of microbiome-based studies, analyzing microbiome patterns is now a hot-topic, finding different fields of application. In particular, the use of machine learning techniques is increasing in microbiome studies, providing deep insights into microbial community composition. In this context, in order to investigate microbial patterns from 16S rRNA metabarcoding data, we explored the effectiveness of Association Rule Mining (ARM) technique, a supervised-machine learning procedure, to extract patterns (in this work, intended as groups of species or taxa) from microbiome data. ARM can generate huge amounts of data, making spurious information removal and visualizing results challenging. Our work sheds light on the strengths and weaknesses of pattern mining strategy into the study of microbial patterns, in particular from 16S rRNA microbiome datasets, applying ARM on real case studies and providing guidelines for future usage. Our results highlighted issues related to the type of input and the use of metadata in microbial pattern extraction, identifying the key steps that must be considered to apply ARM consciously on 16S rRNA microbiome data. To promote the use of ARM and the visualization of microbiome patterns, specifically, we developed microFIM (microbial Frequent Itemset Mining), a versatile Python tool that facilitates the use of ARM integrating common microbiome outputs, such as taxa tables. microFIM implements interest measures to remove spurious information and merges the results of ARM analysis with the common microbiome outputs, providing similar microbiome strategies that help scientists to integrate ARM in microbiome applications. With this work, we aimed at creating a bridge between microbial ecology researchers and ARM technique, making researchers aware about the strength and weaknesses of association rule mining approach.

Link to OA paper: https://www.frontiersin.org/articles/10.3389/fbinf.2021.794547/full
Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition
Authors: Gerrick Elias
Published: September 2024

Commensal protists have historically been overlooked as members of the gut microbiota, but recent studies have highlighted the dominant effects of these commensals on the gut ecosystem. In particular, protists in the Parabasalia phylum reshape the intestinal immune landscape and influence host susceptibility to both infectious and inflammatory diseases. However, the mechanisms used by these protists to shape the gut environment remain poorly understood. Here, we identify a new species of commensal parabasalid in the mouse intestine, Tritrichomonas casperi. We find that metabolic differences between T. casperi and the closely related species Tritrichomonas musculis modulate their effects on host immunity and determine their ecological niche within the microbiota. First, we investigate metabolic output of these commensal parabasalids using genomic and metabolomic analysis. This reveals species-level differences in excretion of the tuft cell activating metabolite succinate, which causes differential remodeling of the immune system in the small intestine. Next, we investigate protist metabolic input by manipulating dietary fiber intake, as well as developing in vitro culture. This reveals that whereas T. musculis preferentially relies on dietary polysaccharides, T. casperi uses host mucus glycans as a carbon source. These carbon source preferences lead to differential competition with commensal bacteria in the intestine, including Bacteroidales spp. and Akkermansia muciniphila. These trans-kingdom interactions can in turn suppress protist-induced intestinal immune responses in a diet-dependent manner. Finally, we explore the diversity of commensal protists in humans by examining parabasalids in the microbiomes of both industrialized and non-industrialized populations. We identify multiple new species of commensal parabasalids in the microbiomes of non-industrialized populations, including novel human-associated tritrichomonads that are closely related T. musculis and T. casperi. Altogether, our findings elucidate how commensal parabasalid metabolism acts as a focal point for complex interactions with the host immune system, commensal bacteria, and diet, to impact intestinal immunity and host health.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.08.26.505490v2
Ethical dimensions of microbiome research
Authors: Manara Serena
Published: September 2024

Panel discussion of the Ethical dimensions of microbiome research event
Mating system and environment predict the direction and extent of introgression in incipient Clarkia species
Authors: Sianta Shelley
Published: September 2024

Introgression is pervasive across the tree of life, but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well-understood. Here, we used 200 genomes and a 15-year site-specific environmental dataset to investigate the effect of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser’s admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.
Abscisic acid acts essentially on stomata, not on xylem, to improve drought tolerance
Authors: Haverroth Eduardo
Published: September 2024

Drought resistance is essential for plant production under water-limiting environments. Abscisic acid (ABA) plays a critical role in stomatal function during drought but its impact on hydraulic function beyond the stomata is less studied. We selected four tomato genotypes differing in their ability to accumulate ABA to investigate its role in drought-induced dysfunction. All genotypes displayed similar leaf and stem embolism resistance, along with comparable leaf hydraulic resistance. The only difference was observed between the two extreme genotypes: sitiens (sit; a strongly ABA-deficient mutant) and sp12 (a transgenic line that constitutively over-accumulates ABA). The water potential inducing 50% embolism was 0.25 MPa lower in sp12 than in sit. Maximum stomatal and minimum leaf conductances were considerably lower in plants with higher ABA biosynthesis (WT and sp12). Variations in gas exchange were associated with both ABA levels and differences in stomatal density and size. Plants with higher ABA biosynthesis exhibited lower water loss, delaying lethal water potentials associated with embolism during drought. In conclusion, ABA does not impact xylem embolism resistance; instead, its primary mechanism for enhancing drought tolerance involves reducing water loss, thus delaying dehydration and hydraulic dysfunction.
Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial
Authors: Jama Hamdi
Published: September 2024

Fibers remain undigested until they reach the colon, where some are fermented by gut microbiota, producing metabolites called short-chain fatty acids (SCFAs), such as acetate and butyrate1. SCFAs lower blood pressure in experimental models2,3,4,5, but their translational potential is unknown. Here we present the results of a phase II, randomized, placebo-controlled, double-blind cross-over trial (Australian New Zealand Clinical Trials Registry ACTRN12619000916145) using prebiotic acetylated and butyrylated high-amylose maize starch (HAMSAB) supplementation6. Twenty treatment-naive participants with hypertension were randomized to 40 g per day of HAMSAB or placebo, completing each arm for 3 weeks, with a 3-week washout period between them. The primary endpoint was a reduction in ambulatory systolic blood pressure. Secondary endpoints included changes to circulating cytokines, immune markers and gut microbiome modulation. Patients receiving the HAMSAB treatment showed a clinically relevant reduction in 24-hour systolic blood pressure independent of age, sex and body mass index without any adverse effects. HAMSAB increased levels of acetate and butyrate, shifted the microbial ecosystem and expanded the prevalence of SCFA producers. In summary, a prebiotic intervention with HAMSAB could represent a promising option to deliver SCFAs and lower blood pressure in patients with essential hypertension.

Link to paper: https://www.nature.com/articles/s44161-022-00197-4
Strain-specific gene function prediction and the Human Microbiome Bioactives Resource
Authors: Huttenhower Curtis
Published: September 2024

Most genetic material encountered in microbial communities - including the human microbiome - remains both uncharacterized and, often, strain-specific. This leaves a tremendous gap in translating microbiome science to personalized biomarkers and therapies. While multi-omic studies represent a promising means of prioritizing leads for validation, this still leaves thousands of molecular targets for most phenotypes of interest. The Human Microbiome Bioactives Resource (HMBR) provides a set of computational and experimental protocols for accelerating these tasks, including the identification of “bioactive” strains, microbial proteins, and chemical products from the human gut, as well as newly predicting function for uncharacterized genes and metabolites. These have proven effective in applications as diverse as the inflammatory bowel diseases (IBD, in a meta-analysis spanning over 8,700 metagenomes) or companion animal nutrition (employing almost 2,500 canine and feline gut samples). In an end-to-end example linking metagenomics, metatranscriptomics, metabolomics, inflammation phenotypes, and drug treatment, we have specifically identified a subset of microbial gene families responsible for 5-ASA inactivation, the leading cause of progression to second-line treatments in IBD. Together, this family of approaches provides multiple new avenues for identifying molecular activities responsible for microbiome-phenotype associations.
Influence of host genetics in shaping the rumen bacterial community in beef cattle
Authors: Abbas Waseem
Published: September 2024

In light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These regions were associated with the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) associated with both related and unrelated taxa. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host. This study demonstrates that host genetics affects rumen bacterial community composition.
Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia
Authors: Tadege Getnet Tesfaw
Published: September 2024

Introduction: Diarrhea claims about 500,000 lives annually among children under five years of age and about 90% of those deaths occur in Sub-Saharan Africa and South Asia. Childhood mortality due to acute diarrhea (AD; less than 7 days of duration) is decreasing, but prolonged (ProD; 7-13 days of duration) and persistent (PD; more than 14 days of duration) diarrhea combined (ProPD) are responsible for increased morbidity and mortality in low- and middle- income countries (LMICs).
Objectives: This study aimed to characterize the gut microbiota (GM) composition of children with acute diarrhea (AD) and prolonged or persistent diarrhea (ProPD) by comparing GM composition between these two groups and with non-diarrheal controls in a case-control study.
Methods: The study included fecal samples from 1321 children 0-59 months old. After preprocessing based on sequencing depth, we analyzed the GM of 1313 children comparing 554 AD cases, 95 ProPD cases, and 663 frequency matched, non-diarrheal controls. All children were enrolled from Jimma, Ethiopia. The GM composition was determined using 16S rRNA gene (V4 region) amplicon sequencing. The observed zero-radius Operational Taxonomic Units (zOTUs) and Shannon diversity index were assessed, and Bray-Curtis dissimilarity metrics were generated and differences between groups evaluated by PERMANOVA. DESeq2 was used to determine taxa being differentially abundant between diarrhea subcategories and non-diarrheal controls.
Results: All diarrhea cases (AD and ProPD) combined and each group separately were associated with a decrease in bacterial diversity compared to non-diarrheal controls. Relative to non-diarrheal controls, the GM of children with AD or ProPD was enriched in Escherichia spp., Campylobacter spp., and Streptococcus spp. The GM of children with AD or ProPD was characterized by a decreased relative abundance of Prevotella copri, Faecalibacterium prausnitzii and Dialister succinatiphilus compared to non-diarrheal controls. Similarly, compared to AD cases, ProPD cases were characterized by a decreased relative abundance of important gut commensals such as F. prausnitzii, Akkermansia muciniphila, Eubacterium hadrum and Blautia spp.
Conclusion: The GM of children with AD and ProPD was enriched in putative pathogens as well as facultative anaerobes, while obligate anaerobes were reduced. The GM of children with ProPD was characterized by a more pronounced reduction of obligate anaerobic gut commensals compared to AD, suggesting that prolonged duration of diarrhea is accompanied by a depletion of healthy gut commensals. This indicates a potential role for targeted dietary supplements to restore gut eubiosis and/ or the use of next generation probiotics to improve ProPD treatment.
Data-driven prediction of colonization outcomes for complex microbial communities
Authors: Wu Lu
Published: September 2024

Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.