Microbiome Community Research Articles

The roles of ABCB1/P-glycoprotein drug transporters in regulating gut microbes and inflammation: insights from animal models, old and new.

Commensal enteric bacteria have evolved systems that enable growth in the ecologic niche of the host gastrointestinal tract. Animals evolved parallel mechanisms to survive the constant exposure to bacteria and their metabolic by-products. We propose that drug transporters encompass a crucial system to managing the gut microbiome. Drug transporters are present in the apical surface of gut epithelia. They detoxify cells from small molecules and toxins (xenobiotics) in the lumen. Here, we review what is known about commensal structure in the absence of the transporter ABCB1/P-glycoprotein in mammalian models. Knockout or low-activity alleles of ABCB1 lead to dysbiosis, Crohn's disease and ulcerative colitis in mammals. However, the exact function of ABCB1 in these contexts remain unclear. We highlight emerging models-the zebrafish Danio rerio and sea urchin Lytechinus pictus-that are poised to help dissect the fundamental mechanisms of ATP-binding cassette (ABC) transporters in the tolerance of commensal and pathogenic communities in the gut. We and others hypothesize that ABCB1 plays a direct role in exporting inflammatory bacterial products from host epithelia. Interdisciplinary work in this research area will lend novel insight to the transporter-mediated pathways that impact microbiome community structure and accelerate the pathogenesis of inflammatory bowel disease when perturbed. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Prebiotic inulin ameliorates SARS-CoV-2 infection in hamsters by modulating the gut microbiome

Current treatment options for COVID-19 are limited, with many antivirals and immunomodulators restricted to the most severe cases and preventative care limited to vaccination. As the SARS-CoV-2 virus and its increasing variants threaten to become a permanent fixture of our lives, this new reality necessitates the development of cost-effective and accessible treatment options for COVID-19. Studies have shown that there are correlations between the gut microbiome and severity of COVID-19, especially with regards to production of physiologically beneficial short-chain fatty acids (SCFAs) by gut microbes. In this study, we used a Syrian hamster model to study how dietary consumption of the prebiotic inulin affected morbidity and mortality resulting from SARS-CoV-2 infection. After two weeks of observation, we discovered that inulin supplementation attenuated morbid weight loss and increased survival rate in hamster subjects. An analysis of microbiome community structure showed significant alterations in 15 genera. Notably, there were also small increases in fecal DCA and a significant increase in serum DCA, perhaps highlighting a role for this secondary bile acid in conferring protection against SARS-CoV-2. In light of these results, inulin and other prebiotics are promising targets for future investigation as preventative treatment options for COVID-19.

Modulating cecal microbiome and in silico amino acid metabolism of sanguinarine-based isoquinoline alkaloids supplements in natural heat stress broiler

Broilers reared under tropical conditions are exposed to Heat Stress (HS) yielding adverseness in production. The study aimed to evaluate the effect of plant-derived sanguinarine-based Isoquinoline alkaloids (IQ) on integrating performance of growth with the cecal microbiome and functional metabolism profiles of amino acid metabolism for either precision nutrition or productivity promotion using nutrition strategies with intestinal microecological balance in broilers of 14-and 35-day of age under HS conditions. IQ significantly improved performance, body weight, average daily weight gain, feed intake, and mortality. IQ significantly modulated the cecum microbiome (14- and 35-dayo of age) by enriching microbiome diversity with increase in Bacteriodetes and Cyanobacteria, but decrease in Firmicutes and Proteobacteria. It was found on 14-day of age that abundances of Turicibactor sanguinis, Lactobacillus salivarious, Lactobacillus sacidophilus, and Akkermansia municiphila in the cecum of boiler fed with IQ60 were higher than in that of the control group. While abundances of Enteroccucus cecorum, Enteroccuus villorum, Escherichia fergusonii, and Helicobacter pullorum were lower in broiler fed with IQs demonstrating the potential to suppress Antimicrobial-Resistant (AMR) reservoirs in the cecum. IQs significantly increased amino acid metabolism namely, l-arginine degradation VII and l-tryptophan degradation I, l-tryptophan degradation VI on day 14, and l-alanine degradation VII, l-tryptophan biosynthesis, l-methionine biosynthesis I, l-methionine salvage cycle, and l-threonine degradation II on day 35 (Kruskal-Wallis p-value < 0.05) in which positively correlated with BW and FI but negative correlation with FCR (Pearson correlation, P < 0.05). It is the first finding that IQs potentially modulated the crosstalk between host and microbiota via the microbiome-gut-brain axis for gut homeostasis by improving Turicibacter sanguini, that promoted serotonin biosynthesis from colonic Enterochromaffin Cells (EC) in modulating Gastro-Intestinal tract (GI) motility. It can be concluded that IQ exhibited the potential to modulate cecal microbiota to improve functional amino acid pathways supporting growth performance in stress broilers. The phenotypic activity related to genotype prediction under in silico model of functional microbiome systems with multi-Omics methods relating with microbiome community is worthwhile to be further investigated leading to discovering potential phytogenic compounds for precision feed additives in stress broilers.

MCSS: microbial community simulator based on structure.

De novo assembly plays a pivotal role in metagenomic analysis, and the incorporation of third-generation sequencing technology can significantly improve the integrity and accuracy of assembly results. Recently, with advancements in sequencing technology (Hi-Fi, ultra-long), several long-read-based bioinformatic tools have been developed. However, the validation of the performance and reliability of these tools is a crucial concern. To address this gap, we present MCSS (microbial community simulator based on structure), which has the capability to generate simulated microbial community and sequencing datasets based on the structure attributes of real microbiome communities. The evaluation results indicate that it can generate simulated communities that exhibit both diversity and similarity to actual community structures. Additionally, MCSS generates synthetic PacBio Hi-Fi and Oxford Nanopore Technologies (ONT) long reads for the species within the simulated community. This innovative tool provides a valuable resource for benchmarking and refining metagenomic analysis methods. Code available at: https://github.com/panlab-bio/mcss.

Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana ‘Xtreme Red’

BackgroundThe microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome.ResultsImpatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate.ConclusionsIn container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.

A modified Mediterranean-style diet enhances brain function via specific gut-microbiome-brain mechanisms.

Alzheimer's disease (AD) is a debilitating brain disorder with rapidly mounting prevalence worldwide, yet no proven AD cure has been discovered. Using a multi-omics approach in a transgenic AD mouse model, the current study demonstrated the efficacy of a modified Mediterranean-ketogenic diet (MkD) on AD-related neurocognitive pathophysiology and underlying mechanisms related to the gut-microbiome-brain axis. The findings revealed that MkD induces profound shifts in the gut microbiome community and microbial metabolites. Most notably, MkD promoted growth of the Lactobacillus population, resulting in increased bacteria-derived lactate production. We discovered elevated levels of microbiome- and diet-derived metabolites in the serum as well, signaling their influence on the brain. Importantly, these changes in serum metabolites upregulated specific receptors that have neuroprotective effects and induced alternations in neuroinflammatory-associated pathway profiles in hippocampus. Additionally, these metabolites displayed strong favorable co-regulation relationship with gut-brain integrity and inflammatory markers, as well as neurobehavioral outcomes. The findings underscore the ameliorative effects of MkD on AD-related neurological function and the underlying gut-brain communication via modulation of the gut microbiome-metabolome arrays.

The urogenital microbiome in chronic kidney disease patients on peritoneal dialysis

Introduction and objectivesDiabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters. Materials and methodsMid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3–V4 region of the bacterial 16S rRNA gene. Correlations with the patients’ clinical data and inflammatory profile were performed. ResultsCKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups. Depletion of Gardnerella, Staphylococcus, Corynebacterium, Lactobacillus or Dermabacter populations correlated with CKD-PD patients with history of diabetes, history of peritonitis and altered levels of sCD14. ConclusionsOur results highlight urogenital microbiome as a potential partner and/or marker in the overall health state of CKD-PD patients.

Effects of organic fertilizer from traditional Chinese medicine residues on growth and soil microbial community of Salvia miltiorrhiza by metagenomic technique

Soil microbiome is a key evaluation index of soil health. Previous studies have shown that organic fertilizer from traditional Chinese medicine(TCM)residues can improve the yield and quality of cultivated traditional Chinese medicinal materials. However, there are few reports on the effects of organic fertilizer from TCM residues on soil microbiome. Therefore, on the basis of evaluating the effects of organic fertilizer from TCM residues on the yield and quality of cultivated Salvia miltiorrhiza, the metagenomic sequencing technique was used to study the effects of organic fertilizer from TCM residues on rhizosphere microbiome community and function of cultivated S. miltiorrhiza. The results showed that:(1) the application of organic fertilizer from TCM residues promoted the growth of S. miltiorrhiza and the accumulation of active components, and the above-ground and underground dry weight and fresh weight of S. miltiorrhiza increased by 371.4%, 288.3%, 313.4%, and 151.9%. The increases of rosmarinic acid and salvianolic acid B were 887.0% and 183.0%.(2)The application of organic fertilizer from TCM residues significantly changed the rhizosphere bacterial and fungal community structures, and the microbial community composition was significantly different.(3)The relative abundance of soil-beneficial bacteria, such as Nitrosospira multiformis, Bacillus subtilis, Lysobacter enzymogenes, and Trichoderma was significantly increased by the application of organic fertilizer from TCM residues.(4)KEGG function prediction analysis showed that metabolism-related microorganisms were more easily enriched in the soil environment after organic fertilizer application. The abundance of functional genes related to nitrification and denitrification could also be increased after the application of organic fertilizer from TCM residues. The results of this study provide guidance for the future application of organic fertilizer from TCM residues in the cultivation of traditio-nal Chinese medicinal materials and enrich the content of green cultivation technology of traditional Chinese medicinal materials.

Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing

The exposure of the air microbiome in indoor air posed a detrimental health effect to the building occupants compared to the outdoor air. Indoor air in hospitals has been identified as a reservoir for various pathogenic microbes. The conventional culture-dependent method has been widely used to access the microbial community in the air. However, it has limited capability in enumerating the complex air microbiome communities, as some of the air microbiomes are uncultivable, slow-growers, and require specific media for cultivation. Here, we utilized a culture-independent method via amplicon sequencing to target the V3 region of 16S rRNA from the pool of total genomic DNA extracted from the dust samples taken from hospital interiors. This method will help occupational health practitioners, researchers, and health authorities to efficiently and comprehensively monitor the presence of harmful air microbiome thus take appropriate action in controlling and minimizing the health risks to the hospital occupants. Key features;•Culture-independent methods offer fast, comprehensive, and unbias profiles of pathogenic and non-pathogenic bacteria from the air microbiomes.•Unlike the culture-dependent method, amplicon sequencing allows bacteria identification to the lowest taxonomy levels.

Unveiling the connection between gut microbiome and metabolic health in individuals with chronic spinal cord injury.

Accumulating evidence has revealed that alterations in the gut microbiome following spinal cord injury (SCI) exhibit similarities to those observed in metabolic syndrome. Considering the causal role of gut dysbiosis in metabolic syndrome development, SCI-induced gut dysbiosis may be a previously unidentified contributor to the increased risk of cardiometabolic diseases, which has garnered attention. With a cross-sectional design, we evaluated the correlation between gut microbiome composition and functional potential with indicators of metabolic health among 46 individuals with chronic SCI. Gut microbiome communities were profiled using next-generation sequencing techniques. Indices of metabolic health, including fasting lipid profile, glucose tolerance, insulin resistance, and inflammatory markers, were assessed through fasting blood tests and an oral glucose tolerance test. We used multivariate statistical techniques (i.e., regularized canonical correlation analysis) to identify correlations between gut bacterial communities, functional pathways, and metabolic health indicators. Our findings spotlight bacterial species and functional pathways associated with complex carbohydrate degradation and maintenance of gut barrier integrity as potential contributors to improved metabolic health. Conversely, those correlated with detrimental microbial metabolites and gut inflammatory pathways demonstrated associations with poorer metabolic health outcomes. This cross-sectional investigation represents a pivotal initial step toward comprehending the intricate interplay between the gut microbiome and metabolic health in SCI. Furthermore, our results identified potential targets for future research endeavors to elucidate the role of the gut microbiome in metabolic syndrome in this population.NEW & NOTEWORTHY Spinal cord injury (SCI) is accompanied by gut dysbiosis and the impact of this on the development of metabolic syndrome in this population remains to be investigated. Our study used next-generation sequencing and multivariate statistical analyses to explore the correlations between gut microbiome composition, function, and metabolic health indices in individuals with chronic SCI. Our results point to potential gut microbial species and functional pathways that may be implicated in the development of metabolic syndrome.

A preliminary study characterizing temporal changes in soil bacterial communities after dismembered bones were buried.

Determining the burial time of skeletal remains is one of the most important issues of forensic medicine. We speculated that the microbiome of gravesoil may be a promising method to infer burial time by virtue of time-dependent. As we know, forensic scientists have established various models to predict the postmortem interval of a decedent based on the changes in body and soil microbiome communities. However, limited data are available on the burial time prediction for bones, especially dismembered bones. In this exploratory study, we initially conducted 16S rRNA amplicon high-throughput sequencing on the burial soil of 10 porcine femurs within a 120-day period and analyzed the changes in soil microbial communities. Compared with the control soil, a higher Shannon index in the microbial diversity of burial soil containing bones was observed. Correlation analysis identified 61 time-related bacterial families and the best subset selection method obtained best subset, containing Thermomonosporaceae, Clostridiaceae, 0319-A21, and Oxalobacteraceae, which were used to construct a simplified multiple linear regression model with a mean absolute error (MAE) of 56.69 accumulated degree day (ADD). An additional random forest model was established based on indicators for the minimum cross-validation error of Thermomonosporaceae, Clostridiaceae, 0319-A21, Oxalobacteraceae, and Syntrophobacteraceae, with an MAE of 55.65 ADD. The produced empirical data in this pilot study provided the evidence of feasibility that the microbial successional changes of burial soil will predict the burial time of dismembered bones and may also expand the current knowledge of the effects of bone burial on soil bacterial communities.

(260) Functional and Taxonomic Urine Microbiome Differences in Men with Abnormal Semen Analysis Parameters

Abstract Introduction Male factors contribute to nearly half of all cases of infertility. Next-generation sequencing technologies have allowed for a more nuanced understanding of the widespread influence of the microbiome on health and human disease. Recent evidence has emerged revealing a potential role for the urinary microbiome in impacting male fertility and subfertility, though studies on this topic are sparse. Objective Here, we explore the complex relationship between the urine microbiome and alterations of SA parameters. Methods Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited. Clinical data and urine samples were collected from the patients and SA was performed. Patients were then stratified according to alterations in SA parameters. Urine samples underwent DNA extraction, PCR amplification and 16S rRNA sequencing. Taxonomic microbiome community profiling was performed. Predictive metagenomics was performed using Tax4Fun2 with reference to the KEGG database. Results N = 73 participants were included in the study and were stratified based on alterations, or lack thereof, in SA parameters. Men with abnormal sperm motility (N = 27) showed a higher abundance of urine Dialister micraerophilus (p = 0.0322) compared to those with normal sperm motility (N = 46). This relationship persisted on canonical correlational analysis (r = 0.439, p = 0.0114). Furthermore, when stratifying by sperm motility, nine differentially abundant pathways emerged from predictive metagenomic analysis including pathways critical for basic microbial cell functioning (intermediary metabolism pathways, FoxO signaling, longevity regulating pathways) in addition to pathways synthesizing and breaking down potentially bioactive metabolites (notably long- and short-chain fatty acid metabolism). Men with abnormal sperm concentration (N = 20) showed a lower abundance of urine Enterococcus faecalis (p = 0.0121) and urine Staphylococcus aureus (p = 0.0375), compared to those with normal sperm concentration (N = 53). These findings are outlined in the differential abundance box plots generated from the Analysis of composition of Microbiota with Bias Correction (ANCOM-BC) in Figure 1 and the differential abundance box plots from the predictive functional analysis in Figure 2. Conclusions Our exploratory analysis suggests a role for not just an altered microbial taxonomic profile but also an altered functional profile in men with abnormal SA parameters. These changes in SA parameters may come about through differences in urine microbial metabolite production including short-chain fatty acids or byproducts of intermediary metabolic processes such as those that may contribute to a pro-inflammatory microenvironment. These findings appear to be aligned with the very limited number of studies exploring similar lines of inquiry. These pathways and microbial communities may represent potential therapeutic targets. Further, more mechanistic, investigations are necessary. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: MicrogenDx, Metuchen Pharmaceuticals, Antares Pharma, Boston Scientific, and Endo Pharmaceuticals.

(076) Semen Microbiome Differences in Men with Abnormal Semen Analysis Parameters

Abstract Introduction Approximately 15% of couples struggle with infertility, of which half can be attributed to male factors. Recent advances in next-generation sequencing technologies have augmented our understanding of human health and disease by allowing for accurate and efficient characterization of the human microbiome. A small, albeit growing body of literature suggests a role for the semen microbiome in impacting male fertility and subfertility. Objective Here, we explore the complex relationship between the semen microbiome and alterations of SA parameters. Methods Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited. Clinical data and semen samples were collected from the patients and SA was performed. Patients were then stratified according to alterations in SA parameters. Semen samples underwent DNA extraction, PCR amplification and 16S rRNA sequencing. Taxonomic microbiome community profiling was performed. Results N = 73 participants were included in the study and were stratified based on alterations, or lack thereof, in SA parameters. Men with abnormal sperm motility (N = 27) showed a three-fold higher abundance of Lactobacillus iners (p = 0.0464) compared to those with normal sperm motility (N = 46). This relationship persisted on canonical correlational analysis (r = 0.392, p = 0.011). Men with abnormal sperm concentration (N = 20) showed a higher abundance of Paraburkholderia phenazinium (p = 0.0247), Pseudomonas fluorescens (p = 0.0101), and Pseudomonas stutzeri (p = 0.0241), but a lower abundance of Pseudomonas putida (p = 0.00478), compared to those with normal sperm concentration (N = 53). Participants with normal SA parameters (N = 40) showed a lower abundance of Peptoniphilus coxii (p = 0.0469) but a higher abundance of Staphylococcus hominis (p = 0.00335) compared to those with any abnormality in sperm concentration or motility (N = 33). These findings are outlined in the differential abundance box plots generated from the Analysis of composition of Microbiota with Bias Correction (ANCOM-BC) in Figure 1 and the canonical correlational analysis visualized in Figure 2. Conclusions Our results suggest that a small group of microorganisms may play a critical role in observed alterations of SA parameters. Some of these microbes, most notably Lactobacillus iners, have been described extensively within other, fertility-related, contexts, whereas for others, this is the first report where they have been implicated in fertility and subfertility. This is the largest study exploring the relationship between the semen microbiome and abnormalities in SA parameters; our findings provide critical insights that will be important in guiding future, mechanistic investigations. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: MicrogenDx, Metuchen Pharmaceuticals, Antares Pharma, Boston Scientific, and Endo Pharmaceuticals.

Effects of Nitrogen on the Bacterial Microbiome Community of Oocystis borgei, an Alga Widely Used in Marine Aquaculture

In order to investigate the effects of various nitrogen (ammonium) concentrations on the epibiotic bacterial community associated with Oocystis borgei, a metabarcoding sequencing method was employed. The 16S rDNA sequencing and bioinformatic analysis were conducted on cultures of O. borgei that were grown on four different nitrogen element concentrations (2.5, 10, 50, and 100 mg/L), and the differences in the epibiotic bacterial community and functions of O. borgei among different nitrogen concentrations were compared. The results showed that the chlorophyll a content of O. borgei increased with increasing nitrogen concentrations. A total of 43 operational taxonomic units (OTUs) were obtained from the four groups, which were categorized into 7 phyla, 9 classes, 18 orders, 21 families, and 26 genera. Winogradskyella was the dominant genus in the groups with 2.5 and 100 mg/L nitrogen, while Marinobacter and Winogradskyella were relatively abundant in the groups with 50 and 100 mg/L nitrogen. Functional analysis using PICRUST2 showed that the three most abundant gene functions were carbohydrate metabolism, amino acid transport and metabolism, ribosomal structure and biogenesis, and energy production and conversion. BugBase phenotypic analysis revealed that there were no significant differences in phenotypes between the groups with 2.5 and 10 mg/L nitrogen, while the group with 50 mg/L nitrogen exhibited higher abundance in aerobicity, biofilm formation, mobile genetic elements, and stress tolerance phenotypes. Most of the bacteria in this work belonged to the aerobic types. A redundancy analysis (RDA) of environmental factors demonstrated that nitrogen concentration showed a positive correlation with species changes in the groups with 10 and 50 mg/L nitrogen; chlorophyll a exhibited a positive correlation with species changes in the groups with 50 and 100 mg/L nitrogen. Nitrogen concentration significantly influenced the epibiotic bacterial community associated with O. borgei, leading to changes in dominant species and community structure. This study provides important references for understanding the functional characteristics of the epiphytic microbial community of O. borgei and the exploration of specific microorganisms.

Microbiome function and neurodevelopment in Black infants: vitamin B12 emerges as a key factor

ABSTRACT The early life gut microbiome affects the developing brain, and therefore may serve as a target to support neurodevelopment of children living in stressful and under-resourced environments, such as Black youth living on the South Side of Chicago, for whom we observe racial disparities in health. Microbiome compositions/functions key to multiple neurodevelopmental facets have not been studied in Black children, a vulnerable population due to racial disparities in health; thus, a subsample of Black infants living in urban, low-income neighborhoods whose mothers participated in a prenatal nutrition study were recruited for testing associations between composition and function of the gut microbiome (16S rRNA gene sequencing, shotgun metagenomics, and targeted metabolomics of fecal samples) and neurodevelopment (developmental testing, maternal report of temperament, and observed stress regulation). Two microbiome community types, defined by high Lachnospiraceae or Enterobacteriaceae abundance, were discovered in this cohort from 16S rRNA gene sequencing analysis; the Enterobacteriaceae-dominant community type was significantly negatively associated with cognition and language scores, specifically in male children. Vitamin B12 biosynthesis emerged as a key microbiome function from shotgun metagenomics sequencing analysis, showing positive associations with all measured developmental skills (i.e., cognition, language, motor, surgency, effortful control, and observed stress regulation). Blautia spp. also were identified as substantial contributors of important microbiome functions, including vitamin B12 biosynthesis and related vitamin B12-dependent microbiome functions, anti-inflammatory microbial surface antigens, competitive mechanisms against pathobionts, and production of antioxidants. The results are promising with respect to the potential for exploring therapeutic candidates, such as vitamin B12 nutritional or Blautia spp. probiotic supplementation, to support the neurodevelopment of infants at risk for experiencing racial disparities in health.

Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile.

The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short-chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of a butyrogenic pathway(s) in C. difficile coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a C. difficile-inhospitable environment to which C. difficile responds by releasing its diarrheagenic toxins and producing environmentally resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate alters C. difficile virulence in the face of a highly competitive and dynamic gut environment.IMPORTANCEThe gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood, which hinders the development of novel therapeutic interventions for C. difficile infection (CDI). We investigated how C. difficile responds to butyrate, an end-product of gut microbiome community metabolism which inhibits C. difficile growth. We show that exogenously produced butyrate is internalized into C. difficile, which inhibits C. difficile growth by interfering with its own butyrate production. This growth inhibition coincides with increased toxin release from C. difficile cells and the production of environmentally resistant spores necessary for transmission between hosts. Future work to disentangle the molecular mechanisms underlying these growth and virulence phenotypes will likely lead to new strategies to restrict C. difficile growth in the gut and minimize its pathogenesis during CDI.

DECODING MICROBIOME DYSBIOSIS THROUGH METAGENOMIC ALPHA DIVERSITY

Background: Sarcoidosis is a chronic inflammatory disease that can affect multiple organs. The aetiology of sarcoidosis is not fully understood, but there is increasing evidence that the microbiome may play a role. The blood microbiome is a collection of microorganisms that live in the bloodstream. It is a complex and dynamic community that is influenced by a variety of factors, including the host’s lifestyle and pathology. Recent studies have shown that people with sarcoidosis have alterations in their blood microbiome. These alterations include changes in the diversity, richness, and evenness of the microbial community. The abundance measures by which the blood microbiome diversity may detect instances of dysbiosis related to sarcoidosis aetiology. It should be clearly distinguished from microbiome changes related to unspecific inflammation or sepsis. However, the available evidence suggests that the microbiome may be a promising target for therapeutic interventions. Aim: The primary goal of this review was to assess and compare the existing metrics of microbiome composition and diversity as established by metagenomic analyses. Additionally, we aim to elucidate the potential causal relationship between these measures, the phenomenon of blood microbiome dysbiosis and the pathogenesis of sarcoidosis. Conclusion: In the present review, we investigated alpha diversity measures as characteristics of microbiome communities, examining their potential as indicators of dysbiosis, and the probablemechanisms of microbiome participation. A descriptive qualitative comparison was conducted between lung microbiome data of sarcoidosis patients and blood microbiome data of healthy adults. This comparison elucidates common taxa between the two microbiomes and identifies taxa potentially involved in sarcoidosis.

ECCO Pioneer Award Functional assessment of the microbiome in persistent IBD-related psychological symptoms

Abstract Background and Aims It is well established that patients with inflammatory bowel disease (IBD) experience psychological comorbidities, and that these symptoms persist upon remission of the IBD in more than 50% of patients. The mechanisms underlying this clinical association are unknown, which hampers to objectify the problem and limits the possibilities to intelligently consider targeted treatments. We recently observed behavioral anomalies and neuroinflammation in a mouse model of extinguished chronic colitis, enabling the fundamental study of psychological symptoms in IBD. Fueled by technical evolutions to characterize translationally active bacteria at the single-cell level, their importance in colitis, and a proof-of-concept stool transplantation experiment, the purpose of this project is to determine if specific bacterial functions drive persistent neuroinflammation upon IBD remission. Methods First, a state-of-the-art flow-cytometry based method will be used to temporally map translationally active bacteria during the course of extinguished chronic colitis. Second, the same functional microbial analysis will be achieved in human fecal samples of IBD patients in remission before and after treatment for fatigue, and results will be compared with persistent bacterial changes found in mouse flora. Finally, causality of associated bacteria to induce neuroinflammation will be tested by transplantation studies of bacterial communities isolated from the previous tasks. Anticipated Impact This research may impact the field in the short-term by creating solid scientific awareness that psychological comorbidities are intrinsically linked with IBD remission, and by more specifically attributing a role for specific bacterial functions in these symptoms. In addition, the technique applied may open novel insights for the IBD microbiome community. In the medium-term, this project aims to shed light on the actual bacterial mechanisms that lead to neuroinflammation and behavioral anomalies, which in the long-term could help identify biomarkers for diagnostic purposes or microbiome-related targets to design rational therapeutics for patients with IBD suffering from psychological comorbidities.

Dietary lysozyme and avilamycin modulate gut health, immunity, and growth rate in broilers

BackgroundAttempts to use dietary lysozyme (LYZ) as an alternative to antibiotics in broilers have been successful, but further research is needed for effective use. Here, we compared the differences between LYZ and avilamycin (AVI) feed additives for growth performance, gut health and immunity of broilers. One-day old, one hundred and twenty broiler chicks (Ross 308) were randomly allocated into three groups consisting forty birds in each group. Standard diet without supplementation was applied as the control group (I), while the chicks of the other groups were supplemented with 100 mg of AVI per kg diet (AVI, group II), and 90 mg LYZ per kg diet (LYZ, group III) for five consecutive weeks.ResultsBody weight, feed conversion ratio, body weight gain, and European production efficiency factor were markedly (p < 0.05) increased in both AVI and LYZ groups in relation to CON group, but the feed intake and protein efficiency ratio were not affected. Both AVI and LYZ significantly (p < 0.001) upregulated the mRNA expression of ileal interleukin-18 (IL-18), interferon-gamma (IFN-γ), and interleukin-10 (IL-10), interleukin-2 (IL-2), and glutathione peroxidase (GSH-PX) genes compared to CON group. However, IL-2, IL-10, IL-18, and GSH-PX genes were markedly (p < 0.01) upregulated in LYZ compared to the AVI group. LYZ treated group had a significant increase (p < 0.05) in the serological haemagglutination inhibition titers of H5N1 vaccination and a significant decrease (p < 0.0001) in coliform counts compared to control and AVI groups, but all growth parameters were nearly similar between AVI and LYZ groups. The VH and VH/CD were markedly higher in LYZ than AVI and control groups.ConclusionExogenous dietary lysozyme supplementation by a dose of 90 mg/kg broilers’ diet induced better effects on intestinal integrity, fecal bacterial counts, immune response, and growth performance which were comparable to avilamycin. Therefore, dietary lysozyme could safely replace avilamycin in the broiler chickens’ diet. However, further experimental studies regarding the use of lysozyme in commercial broilers, both in vitro and in vivo, targeting more communities of intestinal microbiome and explaining more details about its beneficial effects need to be conducted.

Effects of Bisphenol A and Its Substitute, Bisphenol F, on the Gut Microbiota in Mice

ObjectiveThe aim of this study was to assess the impact of bisphenol A (BPA) and its substitute, bisphenol F (BPF), on the colonic fecal community structure and function of mice. MethodsWe exposed 6–8-week-old male C57BL/6 mice to 5 mg/(kg·day) and 50 μg/(kg·day) of BPA or BPF for 14 days. Fecal samples from the colon were analyzed using 16S rRNA sequencing. ResultsGut microbiome community richness and diversity, species composition, and function were significantly altered in mice exposed to BPA or BPF. This change was characterized by elevated levels of Ruminococcaceae UCG-010 and Oscillibacter and decreased levels of Prevotella 9 and Streptococcus. Additionally, pathways related to carbohydrate and amino acid metabolism showed substantial enrichment. ConclusionMice exposed to different BP analogs exhibited distinct gut bacterial community richness, composition, and related metabolic pathways. Considering the essential role of gut bacteria in maintaining intestinal homeostasis, our study highlights the intestinal toxicity of BPs in vertebrates.