Microbiome Community Research Articles

Critically ill patients will benefit from single isolated laminar-air-flow wards by improving the environmental microbial composition.

Hospital-associated infection (HAI) is an important issue in intensive care units (ICUs). We still lack direct evidence on whether the ICU patients and/or the medical system can benefit from single isolated laminar-air-flow (LAF) wards. High-touched-surface (HTS) swabs from 5 sites in two kinds of wards with different ventilation systems were longitudinally collected for 16S rRNA sequencing and Type IIB restriction site-associated DNA sequencing for Microbiome (2bRAD-M). Samples were collected for 3 months. The clinical data of patients admitted to different wards during the sampling time and the whole year were collected and compared. The α-diversity of single wards with isolated LAF was significantly higher than open regions without LAF (p<0.01). β-diversity analysis showed differences between different wards and similarities among the same region. We also identified 3 genera attributed to the most difference between the two kinds of wards. 2bRAD-M analysis further revealed community divergence among different HTS sites. There was an overlap between HTS microbiome profiling and the clinically cultivated pathogens of patients with HAI. People in single wards had a better outcome than those in open regions (p<0.05), indicating that single wards had a protective effect for critically ill patients. Overall, there was a prominent difference in the microbiome community between single wards and open regions. Single wards had more balanced communities which may lead to better outcomes for patients. For critically ill patients, single ward is recommended when arranging and constructing.

Pregnancy during COVID 19 pandemic associated with differential gut microbiome composition as compared to pre-pandemic.

The first two years of the COVID-19 pandemic and subsequent health mandates resulted in significant disruptions to daily life, creating a period of heightened psychosocial stress in myriad aspects. Understanding the impact of this period on pregnant individuals' bacteriomes is crucial as pregnancy is a period of heightened vulnerability to stress and its sequelae, anxiety and mood disorders, which have been demonstrated to alter gut microbiome composition. In a prospective cohort study (N = 12-26) conducted from February 2019 to August 2021, we examined psychometric responses and rectal microbiome swabs from pregnant individuals. Full-length 16S rRNA sequencing followed by calculation of diversity metrics and relative abundance values were used to interrogate fecal microbiome community composition across pandemic groups. Distinct shifts in bacterial diversity and composition were observed during early to late pregnancy in the pandemic group, including lower relative abundance of pathogenic and lesser-known taxa. However, distribution of stress and depressive symptoms did not significantly differ from the pre-pandemic period while the correlation between stress and depressive symptoms dissipated during the pandemic. Our findings suggest that living through the COVID-19 pandemic altered the gut microbiome of pregnant individuals, independent of perceived stress.

The Gut Microbiome Advances Precision Medicine and Diagnostics for Inflammatory Bowel Diseases

The gut microbiome emerges as an integral component of precision medicine because of its signature variability among individuals and its plasticity, which enables personalized therapeutic interventions, especially when integrated with other multiomics data. This promise is further fueled by advances in next-generation sequencing and metabolomics, which allow in-depth high-precision profiling of microbiome communities, their genetic contents, and secreted chemistry. This knowledge has advanced our understanding of our microbial partners, their interaction with cellular targets, and their implication in human conditions such as inflammatory bowel disease (IBD). This explosion of microbiome data inspired the development of next-generation therapeutics for treating IBD that depend on manipulating the gut microbiome by diet modulation or using live products as therapeutics. The current landscape of artificial microbiome therapeutics is not limited to probiotics and fecal transplants but has expanded to include community consortia, engineered probiotics, and defined metabolites, bypassing several limitations that hindered rapid progress in this field such as safety and regulatory issues. More integrated research will reveal new therapeutic targets such as enzymes or receptors mediating interactions between microbiota-secreted molecules that drive or modulate diseases. With the shift toward precision medicine and the enhanced integration of host genetics and polymorphism in treatment regimes, the following key questions emerge: How can we effectively implement microbiomics to further personalize the treatment of diseases like IBD, leveraging proven and validated microbiome links? Can we modulate the microbiome to manage IBD by altering the host immune response? In this review, we discuss recent advances in understanding the mechanism underpinning the role of gut microbes in driving or preventing IBD. We highlight developed targeted approaches to reverse dysbiosis through precision editing of the microbiome. We analyze limitations and opportunities while defining the specific clinical niche for this innovative therapeutic modality for the treatment, prevention, and diagnosis of IBD and its potential implication in precision medicine.

Irradiance level and elevation shape the soil microbiome communities of Coffea arabica L.

BackgroundThe nexus plant-microbe-environment is essential to understand the ecosystem processes shaping plant health and fitness. Within this triangle, soils and associated microflora are among the key ecosystem’s drivers, underpinning plant productivity and evolution. In this study, we conducted a comprehensive analysis (physicochemical properties, enzyme activities, and taxonomic diversity) of soils under the canopy projection of Coffea arabica trees along a gradient of elevation (600, 800, and 900 m) and shade (0, 50, 100%).ResultsWhile shade had no influence on most parameters, altitude shaped the dynamics of microbial communities. Available phosphorus, soil organic carbon, and nitrate were significantly higher at 800 m, likely due to the higher activities of β-glucosidase and phosphatases at this altitude. Microbial biomass (carbon and nitrogen) and moisture were significantly higher at 600 and 900 m, which might be attributed to the abundance and richness of soil microorganisms. Indeed, metabarcoding analysis revealed a complex pattern of microbial consortia (bacteria, archaea, fungi) at the three altitudes, with the lowest index of richness recorded at 800 m. The highest number of Amplicon Sequence Variants was observed in bacteria, whose functional analysis revealed distinct metabolic adaptations across different altitudes. At 900 m, the main functional attributes favored the responses to environmental stimuli and microbial interactions; at 800 m, the predominant metabolic pathways were related to organic matter, fermentation, and bioremediation; and at the lower 600 m, the pathways shifted towards the breakdown of plant-derived compounds (e.g. geraniol, limonene, and pinene degradation).ConclusionOverall, the results indicate a higher effectiveness of the microbial consortium at 800 m, which might result in better nutrient cycling. The study highlights the importance of canopy shade species and elevation for the composition of microbial consortia in C. arabica, unveiling ecological functions beyond plant health, with implications for bio-based solutions and biotechnology.

The microbiome and metatranscriptome of a panel from the Sarracenia mapping population reveal complex assembly and function involving host influence.

Sarracenia provide an optimal system for deciphering the host-microbiome interactions at various levels. We analyzed the pitcher microbiomes and metatranscriptomes of the parental species, and F1 and F2 generations from the mapping population (Sarracenia purpurea X Sarracenia psittacina) utilizing high-throughput sequencing methods. This study aimed to examine the host influences on the microbiome structure and function and to identify the key microbiome traits. Our quality datasets included 8,892,553 full-length bacterial 16s rRNA gene sequences and 65,578 assembled metatranscripts with microbial protein annotations. The correlation network of the bacterial microbiome revealed the presence of 3-7 distinct community clusters, with 8 hub and 19 connector genera. The entire microbiome consisted of viruses, bacterial, archaea, and fungi. The richness and diversity of the microbiome varied among the parental species and offspring genotypes despite being under the same greenhouse environmental conditions. We have discovered certain microbial taxa that are genotype-enriched, including the community hub and connector genera. Nevertheless, there were no significant differences observed in the functional enrichment analysis of the metatranscriptomes across the different genotypes, suggesting a functional convergence of the microbiome. We found that the pitcher microcosm harbors both rhizosphere and phyllosphere microbiomes within its boundaries, resulting in a structurally diverse and functionally complex microbiome community. A total of 50,424 microbial metatranscripts were linked to plant growth-promoting microbial proteins. We show that this complex pitcher microbiome possesses various functions that contribute to plant growth promotion, such as biofertilization, bioremediation, phytohormone signaling, stress regulation, and immune response stimulation. Additionally, the pitcher microbiome exhibits traits related to microbe-microbe interactions, such as colonization of plant systems, biofilm formation, and microbial competitive exclusion. In summary, the demonstrated taxonomical divergence and functionally convergence of the pitcher microbiome are impacted by the host genetics, making it an excellent system for discovering novel beneficial microbiome traits.

Mechanisms of Electroacupuncture in Alleviating Visceral Hypersensitivity in Post-Infectious Irritable Bowel Syndrome Mice: The Role of GDNF Signaling Pathway and Gut Microbiota

Introduction: Post-infectious irritable bowel syndrome (PI-IBS) is a functional bowel disease that develops following an acute gastrointestinal infection. Electroacupuncture (EA) can regulate the gut microbiota and alleviate visceral hypersensitivity. Glial cell-derived neurotrophic factor (GDNF) is a potential factor in visceral hypersensitivity reactions. The aim of this study was to explore whether EA could alleviate visceral hypersensitivity in PI-IBS by regulating gut microbiota through GDNF signaling. Methods: 2,4,6-trinitrobenzene sulfonic acid was used to induce visceral hypersensitivity in PI-IBS mice. Intestinal visceral sensitivity was assessed by using the abdominal withdrawal reflex (colorectal distention). 16S ribosomal RNA sequencing profiles the gut microbiome community. Results: GDNF can exacerbate the imbalances of the gut microbiota and increase visceral hypersensitivity compared with the model group. Whereas EA treatment increases the richness and diversity of the gut microbiota, decreases differences among species and alleviates visceral sensitivity. Conclusion: EA can alleviate visceral hypersensitivity in PI-IBS by regulating the gut microbiota via GDNF signaling, providing new insights for mechanistic research on EA in PI-IBS treatment.

Microbial diversity in primary endodontic infections: demographics and radiographic characteristics.

To analyze if the microbiome community composition in primary endodontic infections is associated with clinical or radiographic factors. Seventy-one patients with primary endodontic infections were evaluated for percussion tenderness, presence of a sinus tract, presence of caries, sex, probing depth > 4mm, and age. Samples from the root canals were obtained and the microbiome was subsequently characterized by 16S rRNA amplicon sequencing. For the radiographic analysis, a subset of 12 samples with a periapical index (PAI) ≤ 2 were compared with 19 samples with PAI of 5. The Shannon and Chao1 indices were used to measure alpha diversity. Differences in abundances of genera were evaluated using the Kruskal-Wallis test with Bonferroni's correction. Differences in community composition were evaluated using analysis of similarity (ANOSIM) with Bray-Curtis dissimilarity matrices. No significant differences in microbiome composition relative to clinical factors were found using ANOSIM. Teeth within the two categories of periapical index showed a similar number of species richness, and alpha diversity values P > 0.05. Community composition was significantly affected by the periapical index (ANOSIM P = 0.039, R = 0.10). Larger radiographic lesions demonstrated significant increase in Prevotellaceae, Olsenella, and the motile bacteria Oribacterium, Selenomonadaceae spp., and Treponema. Clinical factors associated with apical periodontitis have a limited impact on the root canal microbiome composition. Community composition appears to be affected in teeth with large apical lesions.

Global meta‐analysis reveals the drivers of gut microbiome variation across vertebrates

AbstractShifts in gut microbial diversity and structure are one route by which vertebrate hosts adapt to local environmental conditions. However, recent studies have mostly been limited to a single species, small sample sizes, or restricted geographic ranges. Therefore, drawing a global picture of vertebrate gut microbiome diversity, community structure, and determinants for their adaptive shifts remains to be elucidated. We here collected 6508 samples from 113 vertebrate species covering diverse classes, feeding behaviors, and host habitats based on 16S rRNA gene sequencing. The results showed that host diet pattern had a significant impact on gut microbiome variation, which might drive taxonomic and functional contents of gut microbiome across vertebrates. Of note, the phylum Fusobacteria were enriched in carnivorous vertebrate gut while herbivorous vertebrate gut selectively increased the abundance of Verrucomicrobia. Also, climate factors were strongly associated with gut microbiome variation across vertebrates. Interestingly, we found that the abundance of microbiota belonging to Bacteroidetes increased gradually while the members from Proteobacteria showed a decreasing trend from high‐ to low‐latitude zones, potentially contributing to vertebrate adaptation to local climate condition. Additionally, we comprehensively deciphered the common antibiotic resistomes and their potential mobility between terrestrial vertebrate gut microbiome (n = 487) and their sympatric soil biological environment samples (n = 203) by integrating metagenomic sequencing datasets. Particularly, potential horizontal antibiotic resistance genes (e.g., bacA) transfers were detected between vertebrates gut microbiome and their sympatric soil biological environment. Together, our findings provide new evidence of how external environmental factors affect vertebrate gut microbiome variation.

Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial resistance

Background & AimsCirrhosis complications are often triggered by bacterial infections with multidrug-resistant organisms. Alterations in the gut and oral microbiome in decompensated cirrhosis (DC) influence clinical outcomes. We interrogated: (i) gut and oral microbiome community structures, (ii) virulence factors (VFs) and antimicrobial resistance genes (ARGs) and (iii) oral-gut microbial overlap in patients with differing cirrhosis severity. Methods15 healthy controls (HC), 26 stable cirrhosis (SC), 46 DC, 14 acute-on-chronic liver failure (ACLF) and 14 with severe infection without cirrhosis (NLS) participated. Metagenomic sequencing was undertaken on paired saliva (S) and faecal (F) samples. ‘Salivatypes’ and ‘enterotypes’ based on genera clustering were assessed against cirrhosis severity and clinical parameters. VFs and ARGs were evaluated in oral and gut niches, and distinct resistotypes identified. ResultsSalivatypes and enterotypes revealed a greater proportion of pathobionts with concomitant reduction in autochthonous genera with increasing cirrhosis severity and hyperammonaemia. Increasing overlap between oral and gut microbiome communities was observed in DC and ACLF vs SC and HCs, independent of antimicrobial, beta-blocker and acid suppressant therapies. Two distinct gut microbiome clusters [ENT2/ENT3] harboured genes encoding for the phosphoenolpyruvate:sugar phosphotransferase system (PTS) system and other VFs in DC and ACLF. Substantial ARGs (oral: 1,218 and gut: 672) were detected [575 common to both sites]. The cirrhosis resistome was distinct, with three oral and four gut resistotypes identified, respectively. DiscussionThe degree of oral-gut microbial community overlap, frequency of VFs and ARGs all increment significantly with cirrhosis severity, with progressive dominance of pathobionts and loss of commensals. Despite similar antimicrobial exposure, patients with DC and ACLF have reduced microbial richness compared to NLS, supporting the additive pathobiological effect of cirrhosis. Impact and implicationsThis research underscores the crucial role of microbiome alterations in the progression of cirrhosis in an era of escalating multidrug resistant infections, highlighting the association and potential impact of increased oral-gut microbial overlap, virulence factors, and antimicrobial resistance genes on clinical outcomes. These findings are particularly significant for patients with decompensated cirrhosis and acute-on-chronic liver failure, as they reveal the intricate relationship between microbiome alterations and cirrhosis complications. This is relevant in the context of multidrug-resistant organisms and reduced oral-gut microbial diversity that exacerbate cirrhosis severity, drive hepatic decompensation and complicate treatment. For practical applications, these insights could guide for cirrhosis patients the development of targeted microbiome-based therapeutics and personalised antimicrobial regimens to mitigate infectious complications to improve their clinical outcomes.

Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes

Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.

Influence of Peanut Consumption on the Gut Microbiome: A Randomized Clinical Trial.

Background: Peanut consumption could impact cardiometabolic health through gut microbiota, a hypothesis that remains to be investigated. A randomized clinical trial in Vietnam evaluated whether peanut consumption alters gut microbiome communities. Methods: One hundred individuals were included and randomly assigned to the peanut intervention and control groups. A total of 51 participants were provided with and asked to consume 50 g of peanuts daily, while 49 controls maintained their usual dietary intake for 16 weeks. Stool samples were collected before and on the last day of the trial. After excluding 22 non-compliant participants and those who received antibiotic treatment, 35 participants from the intervention and 43 from the control were included in the analysis. Gut microbiota composition was measured by shotgun metagenomic sequencing. Associations of changes in gut microbial diversity with peanut intervention were evaluated via linear regression analysis. Linear mixed-effects models were used to analyze associations of composition, sub-community structure, and microbial metabolic pathways with peanut intervention. We also performed beta regression analysis to examine the impact of peanut intervention on the overall and individual stability of microbial taxa and metabolic pathways. All associations with false discovery rate (FDR)-corrected p-values of <0.1 were considered statistically significant. Results: No significant changes were found in α- and β-diversities and overall gut microbial stability after peanut intervention. However, the peanut intervention led to lower enrichment of five phyla, five classes, two orders, twenty-four metabolic pathways, and six species-level sub-communities, with a dominant representation of Bifidobacterium pseudocatenulatum, Escherichia coli D, Holdemanella biformis, Ruminococcus D bicirculans, Roseburia inulinivorans, and MGYG-HGUT-00200 (p < 0.05 and FDR < 0.1). The peanut intervention led to the short-term stability of several species, such as Faecalibacterium prausnitzii F and H, and a metabolic pathway involved in nitrate reduction V (p < 0.05; FDR < 0.1), known for their potential roles in human health, especially cardiovascular health. Conclusions: In summary, a 16-week peanut intervention led to significant changes in gut microbial composition, species-level sub-communities, and the short-term stability of several bacteria, but not overall gut microbial diversity and stability. Further research with a larger sample size and a longer intervention period is needed to confirm these findings and investigate the direct impact of gut-microbiome-mediated health effects of peanut consumption. Trial registration: The International Traditional Medicine Clinical Trial Registry (ITMCTR). Registration number: ITMCTR2024000050. Retrospectively Registered 24 April 2024.

Abstract C057: Pilot study of vaginal microbiome profiles among Black and White endometrial cancer survivors

Abstract Background: Lower vaginal microbiome diversity, and specifically a Lactobacillus crispatis-dominant vagitype, is associated with more favorable health outcomes. Racial variation in the vaginal microbiome has been reported in some studies, including gynecologic cancers. Racial disparities in endometrial cancer 5-year survival are stark—62% for Black women vs. 83% for White women. Cancer treatments can acutely impact the microbiome of surrounding tissues with potential impacts on quality of life in survivorship, including sexual function. The objectives of this pilot research were to assess the feasibility of self-sampling and variation in vaginal microbiome communities by race, cancer treatment, and sexual function among endometrial cancer survivors. Methods: Endometrial cancer survivors (N=50, mean=11 months from diagnosis) enrolled in the Carolina Endometrial Cancer Study were mailed Genotek vaginal microbiome self-collection kits and the validated Sexual Function-Vaginal Changes Questionnaire (SVQ) before a nurse home visit. Microbiota profiles were characterized by bacteria 16S rRNA amplicon sequencing. Vagitypes were classified as Lactobacillus-dominant and other based on relative abundance (&amp;gt;50% vs. ≤50%) and Ward hierarchical clustering. Results: Overall, 48 vaginal samples were obtained. We excluded samples from women who reported antibiotic use within the last month (N=8) or were missing treatment data (N=6), leaving 34 samples. Of these, 47% were from Black survivors and 53% from White. Cancer treatments were categorized as surgery only (47%) vs. any chemotherapy or radiation (53%); and did not vary by race (p &amp;gt;.9). Black women did not have statistically significant different alpha (Shannon p=0.9) or beta (p=0.4) diversity, or a differential proportion of Lactobacillus dominant vagitype (59% vs. 41%, p=0.3) compared to White women. Alpha (Shannon p=0.04) and beta (p=0.004) diversity varied by cancer treatment with higher microbial diversity after chemotherapy or radiation compared to surgery alone. In the surgery only group, 63% of samples were Lactobacillus dominant, compared to 17% among the chemotherapy or radiation group (p=0.006). We examined cancer treatment associations in analyses restricted to the more favorable endometroid histology (N=25), as surgery alone is associated with endometrioid histology and better prognosis. In this subgroup, 57% (8/14) of women treated with surgery only had Lactobacillus-dominant vagitypes compared to 27% (3/11) in the chemotherapy/ radiation group (p=0.1). Lactobacillus-dominant vagitype was not associated with SVQ scales (global satisfaction; changes in intimacy or interest; dryness; pain). Conclusion: Self-collection of vaginal microbiome samples is feasible in cancer survivors. In our study, Lactobacillus-dominant vagitypes were less abundant among women who were treated with more intensive cancer therapies and did not vary by race or sexual function. Radiation and chemotherapy for endometrial cancer may affect vaginal microbiome composition after treatment ends. Citation Format: Mu Jin, Tope Keku, Nikki McCoy, Jordyn Brown, Jamie Hunter, Victoria Bae-Jump, M. Andrea Azcarate-Peril, Stephanie Engle, Andy Olshan, Hazel B Nichols. Pilot study of vaginal microbiome profiles among Black and White endometrial cancer survivors [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C057.

451 Establishing producer research sites for the development of beef and bison climate-smart agriculture

Abstract Greenhouse gas (GHG) emissions and livestock production are topics that are increasingly intertwined. While livestock production is frequently presented as harmful to the environment, this perception fails to consider the carbon sequestration that takes place in livestock grazing systems and the role that grazing ruminants have in maintaining healthy grassland ecosystems. Grazing lands, which are often unsuited to row crop agriculture, are estimated to account for 25% of the global soil sequestration potential for soil carbon storage. Grazing livestock producers are often overlooked in the GHG reduction conversation, despite over 70% of beef GHG emissions being attributed to the cow-calf sector, which is primarily grazing. Furthermore, there is a relative lack of data surrounding the implementation of climate-smart agriculture practices on grazing operations and a lack of cost-effective methods to measure carbon/GHG sinks and sources on these landscapes. The potential climate benefits are considerable, with nearly 940 million acres of rangelands in the U.S. supporting forage-based livestock production. South Dakota State University recently received funding to support a large-scale climate-smart project focused on grazing beef and bison. For this project, we are utilizing the Cottonwood Field Station that has over 80 yr of historical grazing data, along with six grazing beef and bison ranching operations in the Northern Great Plains. The work on these ranches will focus on measuring and monitoring the impacts of climate-smart NRCS land practices, including cover crops, improved pasture and range seedings, prescribed grazing, and prescribed burning. A significant focus will be extensive, annual soil sampling across these operations to continuously monitor changes in soil organic carbon, bulk density, texture, pH, and soil microbiome community profiles. Each operation will have GreenFeed methane pasture units deployed for 5 yr to monitor changes in beef cattle and bison methane emissions in response to climate-smart practice adoption. We are also assessing biodiversity pre and post climate-smart practice adoption, as biodiversity improvements may be one of the most overlooked and yet most important responses to climate-smart land practice implementation. Over the duration of this project, a large-scale, comprehensive data collection will be achieved and used to refine GHG and carbon sequestration estimates associated with range livestock systems. Data resulting from this project will be used to inform research protocols and prediction models, fill knowledge gaps, and shape science-based discussions and marketing strategies for climate-smart agricultural commodities.

A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples.

Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g., BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB), allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 93.1%, a specificity of 90%, a negative predictive value of 93.4%, and a positive predictive value of 89.6% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP), and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7000 human vaginal samples with this pipeline and described general findings and comparisons to US census data.

Metagenomic insights into traditional fermentation of rice-based beverages among ethnic tribes in southern Assam, Northeast India.

Traditional fermented foods have long been recognized for their numerous health benefits along with their potential to aid in the treatment of gastrointestinal disorders. These fermented foods have been shown to promote gut health and contribute to a longer, healthier life. The high-throughput sequencing using the Illumina MiSeq platform was employed to investigate the microbiome communities of rice-based fermented beverages consumed by ethnic tribes in Southern Assam, namely Zeme Naga, Dimasa Kachari, Hmar, Karbi and Tea tribes. The fermented rice-based beverages were highly predominated by Firmicutes, Bacteroides, Proteobacteria, and Actinobacteria exhibiting the highest relative abundance across all tribes. At genus level, significant abundance of pediococcus, lactobacillus, bacillus, leuconostoc, acetobacter, staphylococcus, delftia, erwinia, klebsiella and chrysebacterium were found amongst these ethnic tribes. Understanding the fermented food microbiome will help to know the relationships between microbial communities and their effect on health of humans amongst the tribes. Furthermore, the use of these fermented products could provide enhanced health benefits to southern Assam region of India.

Unveiling the Intricate Link Between Anaerobe Niche and Alzheimer Disease Pathogenesis.

Dysbiosis within microbiomes has been increasingly implicated in many systemic illnesses, such as cardiovascular disease, metabolic syndrome, respiratory infections, and Alzheimer disease (Ad). The correlation between Ad and microbial dysbiosis has been repeatedly shown, yet the etiologic cause of microbial dysbiosis remains elusive. From a neuropathology perspective, abnormal (often age-related) changes in the brain, associated structures, and bodily lumens tend toward an accumulation of oxygen-depleted pathologic structures, which are anaerobically selective niches. These anaerobic environments may promote progressive change in the microbial community proximal to the brain and thus deserve further investigation. In this review, we identify and explore what is known about the anaerobic niche near or associated with the brain and the anaerobes that it is harbors. We identify the anaerobe stakeholders within microbiome communities and the impacts on the neurodegenerative processes associated with Ad. Chronic oral dysbiosis in anaerobic dental pockets and the composition of the gut microbiota from fecal stool are the 2 largest anaerobic niche sources of bacterial transference to the brain. At the blood-brain barrier, cerebral atherosclerotic plaques are predominated by anaerobic species intimately associated with the brain vasculature. Focal cerebritis/brain abscess and corpora amylacea may also establish chronic anaerobic niches in direct proximity to brain parenchyma. In exploring the anaerobic niche proximal to the brain, we identify research opportunities to explore potential sources of microbial dysbiosis associated with Ad.

Testosterone treatment impacts the intestinal microbiome of transgender individuals.

Medical modulation of sex hormone levels is a cornerstone of treatment for many conditions that impact well-being, including cancer, fertility/infertility, gender dysphoria, and chronic metabolic diseases such as diabetes and obesity. The microbial residents of the intestine, known as the microbiota, interact with sex hormones in the intestine, and there is correlative evidence that this interaction is bidirectional. Based on these published findings, we hypothesized that transgender individuals receiving exogenous testosterone as part of their gender-affirming medical treatment might undergo changes in their intestinal microbiome. To test this, we collected 26 stool samples from nine individuals before and up to 8 months after initiation of treatment with exogenous testosterone and subjected these samples to metagenomic analysis. While no species were significantly associated with the duration of testosterone therapy, pathways that generate glutamate increased in abundance, while those that consume glutamate decreased. Glutamate is a precursor of arginine, and testosterone is known to increase levels of arginine and its metabolites in the plasma. We hypothesize that testosterone increases the uptake of glutamate by enterocytes, thus decreasing access of the microbiota to this amino acid. While this pilot study establishes the impact of testosterone therapy on the intestinal microbiome, a more comprehensive study is necessary to establish the impact of testosterone-driven metagenomic shifts on the stool metatranscriptome, the stool metabolome, and the plasma metabolome.IMPORTANCEThe human intestine is inhabited by a large community of microbes known as the microbiome. Members of the microbiome consume the diet along with their human host. Thus, the metabolomes of the host and microbe are intricately linked. Testosterone alters the plasma metabolome. In particular, plasma levels of arginine and its metabolites and testosterone are positively correlated. To investigate the impact of exogenous testosterone on the microbiome, we analyzed the stool metagenomes of transgender individuals before and after the initiation of testosterone treatment. In this pilot project, we found a modest impact on the microbiome community structure but an increase in the abundance of metabolic pathways that generate glutamate and spare glutamate consumption. We propose that the host uses glutamate to generate arginine, decreasing the amount available for the microbiome.

Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients

ObjectiveGut microbiome composition is associated with multiple diseases, but relatively little is known about its relationship with long-term outcome measures. While gut dysbiosis has been linked to mortality risk in...

Specific gut microbiome's role in skin pigmentation: insights from SCARB1 mutants in Oujiang colour common carp.

Beyond the pivotal roles of the gut microbiome in initiating physiological processes and modulating genetic factors, a query persists: Can a single gene mutation alter the abundance of the gut microbiome community? Not only this, but the intricate impact of gut microbiome composition on skin pigmentation has been largely unexplored. Based on these premises, our study examines the abundance of lipase-producing gut microbes about differential gene expression associated with bile acid synthesis and lipid metabolism-related blood metabolites in red (whole wild) and white (whole white wild and SCARB1-/- mutant) Oujiang colour common carp. Following the disruption of the SCARB1 gene in the resulting mutant fish with white body colour (SCARB1-/-), there is a notable decrease in the abundance of gut microbiomes (Bacillus, Staphylococcus, Pseudomonas, and Serratia) associated with lipase production. This reduction parallels the downregulation seen in wild-type white body colour fish (WW), as contrasting to the wild-type red body colour fish (WR). Meanwhile, in SCARB1-/- fish, there was a downregulation noted not only at the genetic and metabolic levels but also a decrease in lipase-producing bacteria. This consistency with WW contrasts significantly with WR. Similarly, genes involved in the bile acid synthesis pathway, along with blood metabolites related to lipid metabolism, exhibited downregulation in SCARB1-/- fish. The SCARB1 knockout gene blockage led to significant alterations in the gut microbiome, potentially influencing the observed reduction in carotenoid-associated skin pigmentation. Our study emphasizes that skin pigmentation is not only impacted by genetic factors but also by the gut microbiome. Meanwhile, the gut microbiome's adaptability can be rapidly shaped and may be driven by specific single-gene variations.

Hidden in the blow - a matrix to characterise cetaceans’ respiratory microbiome: short-finned pilot whale as case study

Cetaceans are key sentinel species of marine ecosystems and ocean health, being a strategic taxonomic group that evaluates the well-being of aquatic habitats and detects harmful environmental trends. Respiratory diseases are amongst the main causes of death in these animals, so identifying the microbiome community in their exhaled breath condensates (EBC), i.e. blow, has been proposed as a key biomarker for assessing respiratory health. Yet, to characterise microbiomes related to these animals’ respiratory tract and use them as a proxy for health status, it is necessary to develop baseline data on the microorganisms associated with cetaceans. Here, the short-finned pilot whale (SFPW, Globicephala macrorhynchus) was used as a case study to validate the most suitable primer set to explore the prokaryotic diversity of the cetaceans’ respiratory tract. DNA extracted from blow samples (n = 12) of animals off Madeira Island was sequenced to amplify both V3-V4 and V4-V5 hypervariable regions of the 16S rRNA gene, using the same sequencing platform (Illumina MiSeq). Independently of the primer set used, all blows shared Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla in their composition. V3-V4 resulted in a higher diversity of taxa with relative abundance above 1%, whereas the V4-V5 primers captured a higher number of microbial Amplicon Sequence Variants, detecting the rare microbial biosphere with pathogen potential. Additionally, it captured the core microbiome more efficiently. Thus, this study provides a detailed characterisation of SFPW respiratory-associated microbial communities, strengthening the idea of sociality influencing microbiome composition in the respiratory tract. Moreover, it supports the use of blow as a relevant biomarker for the physiological state of the airways in free-ranging cetaceans.