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Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions. [Display omitted] • Biosynthetic gene clusters (BGCs) were discovered from the human gut microbiome • A meta-analysis approach identified BGCs that are enriched in Crohn's disease • Two disease-enriched BGCs produce a unique set of fatty acid amides (ebf - ecf -FAAs) • ebf - ecf -FAAs exist in patient fecal samples and exacerbate colitis in mouse models Elmassry et al. employed computational and experimental approaches to identify gut microbiome-encoded biosynthetic gene clusters that are enriched in Crohn's disease patients and the small molecules they produce, which exacerbated disease when introduced to mouse models of colitis. [ABSTRACT FROM AUTHOR]

The interactions between macronutrients, the human gut microbiome, and their metabolites (short-chain fatty acids) were comprehensively investigated via an in vitro digestion and fermentation model subjected to eight pulse species. 16S rRNA sequencing and taxonomic analysis of pulse digesta fermented for up to 24 h revealed an increase in the relative abundance of gut health-detrimental genera represented by Escherichia-Shigella in kidney bean, soybean, cowpea, chickpea, and black bean samples. In contrast, the relative abundance of health-positive genera, including Bacteroides , Eubacterium , and Akkermansia , was elevated in red bean, mung bean, and Heunguseul. At the same time, the proportion of the pathogenic Escherichia-Shigella decreased. Concurrently, these three species exhibited an increase in microbial diversity as evidenced by the calculation of α -diversity (Shannon index) and β -diversity (Bray-Curtis distance). Despite the lower nutrient contents in the three pulses, represented by carbohydrates, amino acids, and fatty acids, network analysis revealed that the nutrient contents in the pulse digesta possess complex positive or negative correlations with a variety of bacteria, as well as their metabolites. These correlations were more pronounced in red bean, mung bean, and Heunguseul than in the other pulses. It was postulated that the overall potential to nourish gut environments in these species was due to the balance of their nutritional components. The linear regression analysis demonstrated that there was a negative association between carbohydrate and amino acid contents and the increase in Shannon indices. Furthermore, the ratio of carbohydrates to fatty acids and amino acids to fatty acids displayed negative correlations with the diversity increase. The ratio of carbohydrates to amino acids showed a weak positive correlation. It is noteworthy that a diet comprising foods with a balanced nutritional profile supports the growth of beneficial gut microbes, thereby promoting microbial eubiosis. Consistent work on different ingredients is essential for precise insight into the interplay between food and the human microbiome in complex dietary patterns. [ABSTRACT FROM AUTHOR]

Background: The treatment effects are heterogenous across patients due to the differences in their microbiomes, which in turn implies that we can enhance the treatment effect by manipulating the patient's microbiome profile. Then, the coadministration of microbiome-based dietary supplements/therapeutics along with the primary treatment has been the subject of intensive investigation. However, for this, we first need to comprehend which microbes help (or prevent) the treatment to cure the patient's disease. Results: In this paper, we introduce a cloud platform, named microbiome causal machine learning (MiCML), for the analysis of treatment effects using microbiome profiles on user-friendly web environments. MiCML is in particular unique with the up-to-date features of (i) batch effect correction to mitigate systematic variation in collective large-scale microbiome data due to the differences in their underlying batches, and (ii) causal machine learning to estimate treatment effects with consistency and then discern microbial taxa that enhance (or lower) the efficacy of the primary treatment. We also stress that MiCML can handle the data from either randomized controlled trials or observational studies. Conclusion: We describe MiCML as a useful analytic tool for microbiome-based personalized medicine. MiCML is freely available on our web server (http://micml.micloud.kr). MiCML can also be implemented locally on the user's computer through our GitHub repository (https://github.com/hk1785/micml). [ABSTRACT FROM AUTHOR]

Drugs represent our first, and sometimes last, line of defense for many diseases, yet despite decades of research we still do not fully understand why a given drug works in one patient and fails in the next. The human gut microbiome is one of the missing puzzle pieces, due to its ability to parallel and extend host pathways for drug metabolism, along with more complex host–microbiome interactions. Herein, we focus on the well-established links between the gut microbiome and drugs for heart disease and cancer, plus emerging data on neurological disease. We highlight the interdisciplinary methods that are available and how they can be used to address major remaining knowledge gaps, including the consequences of microbial drug metabolism for treatment outcomes. Continued progress in this area promises fundamental biological insights into humans and their associated microbial communities and strategies for leveraging the microbiome to improve the practice of medicine. [ABSTRACT FROM AUTHOR]

This review focuses on the role of microorganisms in promoting health and immune function within school environments. Microbes, including bacteria, viruses, fungi, and other microorganisms, constitute the human microbiome and play a crucial role in various bodily functions and immune system development. The complex interactions between microorganisms and the immune system in schools, where children spend a significant amount of time, are not fully understood. While schools have traditionally emphasized hygiene practices to prevent the spread of infectious diseases, recent research has highlighted the potential consequences of reduced microbial exposure during early life. The "hygiene hypothesis" suggests that limited exposure to microbes in infancy may increase the risk of allergies, asthma, and autoimmune diseases in adulthood. This paper explores the microbial diversity found in schools, the benefits of exposure to different microorganisms, and the implications of hygiene practices on immune system development. It also examines current research on microbial intervention strategies and their potential to influence overall health in schools. Understanding the role of microbes in school environments has implications for public health policies and educational practices, aiming to create healthier and more conducive learning environments for the younger generation. By comprehensively exploring this topic, this review contributes to a broader understanding of the significance of microbes in promoting health and immune function in school settings and its relevance to future health research. A system dynamics approach to understanding the health and immune enhancement in school settings. [ABSTRACT FROM AUTHOR]

Introduction and Objective. Probiotics, defined as live microorganisms that provide health benefits when consumed in sufficient quantities, have gained attention in the sports community. The surge in popularity of long-distance athletic competitions such as marathons, triathlons, and cycling races has led to heightened rivalry and a rising curiosity in strategies to improve sports performance. Studies have suggested that probiotics could be a valuable aid for athletes looking to improve their well-being and overall progress. Methods. A literature review was conducted using PubMed and Google Scholar with search terms like "probiotics", "gut microflora", "probiotics in sport", "human microbiome", "athletic performance", "human microbiome", "diet supplementation" and related variations. Articles published within the last five years were prioritized. Brief description of the state of Knowledge. Probiotic supplementation has been shown to positively impact the health and performance of athletes, primarily through modulation of the microbiota-gut-brain axis. This review examines the influence of probiotic supplements on athletic performance, focusing on their effects on gut microbiota, immune support, mental health, anti-inflammatory properties, and overall performance enhancement. Conclusions. Probiotics have been found to have numerous health benefits within the microbiota-gut-brain axis, making them an emerging area of research in athletes. The aim of this research is to understand the potential impacts on athletes experiencing health issues such as gastrointestinal symptoms, lowered immune system, mental disorders, excessive inflammation, or those looking to improve endurance and performance. [ABSTRACT FROM AUTHOR]

Background The substantial risk for respiratory and invasive infections with Streptococcus pneumoniae (Spn) among people with HIV-1 (PWH) begins with asymptomatic colonization. The frequency of Spn colonization among US adults with and without HIV-1 infection is not well characterized in the conjugate vaccine era. Methods We determined Spn colonization frequency by culture and specific lytA gene quantitative polymerase chain reaction (PCR) and microbiota profile by 16S ribosomal RNA gene sequencing in nasopharyngeal (NP) and oropharyngeal (OP) DNA from 138 PWH and 93 control adults and associated clinical characteristics. Results The frequencies of Spn colonization among PWH and controls did not differ (11.6% vs 8.6%, respectively; P =.46) using combined results of culture and PCR, independent of vaccination or behavioral risks. PWH showed altered microbiota composition (ie, β-diversity; NP: P =.0028, OP: P =.0098), decreased α-diversity (NP: P =.024, OP: P =.0045), and differences in the relative abundance of multiple bacterial taxa. Spn colonization was associated with altered β-diversity in the nasopharynx (P =.011) but not oropharynx (P =.21). Conclusions Despite widespread conjugate vaccine and antiretroviral use, frequencies of Spn colonization among PWH and controls are currently consistent with those reported in the preconjugate era. The persistently increased risk of pneumococcal disease despite antiretroviral therapy may relate to behavioral and immunologic variables other than colonization. [ABSTRACT FROM AUTHOR]

Objective: To comprehensively review and critically assess the literature on microbiota differences between patients with interstitial cystitis (IC)/bladder pain syndrome (BPS) and normal controls and to provide clinical practice guidelines. Materials and methods: In this systematic review, we evaluated previous research on microbiota disparities between IC/BPS and normal controls, as well as distinctions among IC/BPS subgroups. A comprehensive literature search was conducted across PubMed/MEDLINE, EMBASE, Web of Science, and the Cochrane Central Register of Controlled Trials. Relevant studies were shortlisted based on predetermined inclusion and exclusion criteria, followed by quality assessment. The primary focus was identifying specific taxonomic variations among these cohorts. Results: A total of 12 studies met the selection criteria. Discrepancies were adjudicated by a third reviewer. The Newcastle–Ottawa Scale was used to assess study quality. Predominantly, the studies focused on disparities in urine microbiota between IC/BPS patients and normal controls, with one study examining gut microbiota differences between the groups, and two studies exploring vaginal microbiota distinctions. Unfortunately, analyses of discrepancies in other microbiota were limited. Our findings revealed evidence of distinct bacterial abundance variations, particularly involving Lactobacillus, alongside variations in specific metabolites among IC/BPS patients compared to controls. Conclusions: Currently, there is evidence suggesting significant variations in the diversity and species composition of the urinary microbiota between individuals diagnosed with IC/BPS and control groups. In the foreseeable future, urologists should consider urine microbiota dysbiosis as a potential aetiology for IC, with potential clinical implications for diagnosis and treatment. [ABSTRACT FROM AUTHOR]

Background/Objectives: Faecal microbiota transplantation (FMT) is considered a safe and effective therapy for recurrent Clostridioides difficile infection. It is the only current clinical indication for this technique, although numerous clinical research studies and trials propose its potential usefulness for treating other pathologies. Donor selection is a very rigorous process, based on a personal lifestyle interview and the absence of known pathogens in faeces and serum, leading to only a few volunteers finally achieving the corresponding certification. However, despite the high amount of data generated from the ongoing research studies relating microbiota and health, there is not yet a consensus defining what is a "healthy" microbiota. To date, knowledge of the composition of the microbiota is not a requirement to be a faecal donor. The aim of this work was to evaluate whether the analysis of the composition of the microbiota by massive sequencing of 16S rDNA could be useful in the selection of the faecal donors. Methods: Samples from 10 certified donors from Mikrobiomik Healthcare Company were collected and sequenced using 16S rDNA in a MiSeq (Illumina) platform. Alpha (Chao1 and Shannon indices) and beta diversity (Bray–Curtis) were performed using the bioinformatic web server Microbiome Analyst. The differences in microbial composition at the genera and phyla levels among the donors were evaluated. Results: The microbial diversity metric by alpha diversity indexes showed that most donors exhibited a similar microbial diversity and richness, whereas beta diversity by 16S rDNA sequencing revealed significant inter-donor differences, with a more stable microbial composition over time in some donors. The phyla Bacillota and Bacteroidota were predominant in all donors, while the density of other phyla, such as Actinomycota and Pseudomonota, varied among individuals. Each donor exhibited a characteristic genera distribution pattern; however, it was possible to define a microbiome core consisting of the genera Agathobacter, Eubacterium, Bacteroides, Clostridia UCG-014 and Akkermansia. Conclusions: The results suggest that donor certification does not need to rely exclusively on their microbiota composition, as it is unique to each donor. While one donor showed greater microbial diversity and richness, clear criteria for microbial normality and health have yet to be established. Therefore, donor certification should focus more on clinical and lifestyle aspects. [ABSTRACT FROM AUTHOR]

Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.

Abstract Background Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated. Methods In this case–control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation–maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls. Results The α-diversity of dust microorganisms in AR was lower than that in control group (P = 0.034), and the β-diversity indices of microorganisms in nasal cavity (P = 0.020), skin (P = 0.001) and dust (P = 0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score > 2, P

Abstract Background The rapid establishment and persistence of latent HIV-1 reservoirs is one of the main obstacles towards an HIV cure. While antiretroviral therapy supresses viral replication, it does not eradicate the latent reservoir of HIV-1-infected cells. Recent evidence suggests that the human microbiome, particularly the gut microbiome, may have the potential to modulate the HIV-1 reservoir. However, literature is limited and the exact mechanisms underlying the role of the microbiome in HIV immunity and potential regulation of the viral reservoir remain poorly understood. Results Here, we review updated knowledge on the associations between the human microbiome and HIV reservoir across different anatomical sites, including the gut, the lungs and blood. We provide an overview of the predominant taxa associated with prominent microbiome changes in the context of HIV infection. Based on the current evidence, we summarize the main study findings, with specific focus on consistent bacterial and related byproduct associations. Specifically, we address the contribution of immune activation and inflammatory signatures on HIV-1 persistence. Furthermore, we discuss possible scenarios by which bacterial-associated inflammatory mediators, related metabolites and host immune signatures may modulate the HIV reservoir size. Finally, we speculate on potential implications of microbiome-based therapeutics for future HIV-1 cure strategies, highlighting challenges and limitations inherent in this research field. Conclusions Despite recent advances, this review underscores the need for further research to deepen the understanding of the complex interplay between the human microbiome and HIV reservoir. Further integrative multi-omics assessments and functional studies are crucial to test the outlined hypothesis and to identify potential therapeutic targets ultimately able to achieve an effective cure for HIV.

Hana M Sawan,1 Wejdan Shroukh,2 Rana Abutaima,3 Shatha M Al Omari,1 Derar H Abdel-Qader,4 Reem Binsuwaidan5 1Pharmaceutical Sciences Department, Faculty of Pharmacy, Zarqa University, Zqrqa, Jordan; 2Faculty of Pharmacy, Middle East University, Amman, Jordan; 3Faculty of Pharmacy, Zarqa Private University, Zarqa, Jordan; 4Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan; 5Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi ArabiaCorrespondence: Hana M Sawan, Email habusawan@zu.edu.joObjective: This study aimed to assess Jordanian pharmacists’ knowledge of the human microbiome and the impact of their knowledge on their attitudes and practices toward antibiotics and probiotics.Methods: A self-administered survey was designed after reviewing the literature. Participants’ demographics were collected, and questions to evaluate pharmacists’ knowledge, attitudes, and practices toward antibiotic and probiotic dispensing were asked. The data were analyzed using the Statistical Package for the Social Sciences V.26. Pearson correlations and one-way ANOVA were employed to calculate the significance of knowledge, attitudes, and practices. Statistical significance was considered at p < 0.05.Results: Of the 333 respondents, around 75% (n=250) had a high level of general knowledge regarding the human gut microbiome. Almost equal proportions of participants had either intermediate or high levels of knowledge about the role of gut bacteria in health (n=164, 49.2%) (n=166, 49.8%), respectively, while almost two-thirds had an intermediate level of knowledge of the role of gut bacteria in disease (n=197, 59.2%). More than half of the participants had a positive attitude toward antibiotics, probiotics, and the human microbiome (n=179, 53.8%), and the majority (n=239, 71.8%) had an intermediate level of practice with them. There was a significant positive correlation between pharmacists’ general knowledge of the human microbiome and their positive attitudes (r=0.306, p < 0.01) and practices (r=0.331, p < 0.01) toward antibiotics and probiotics.Conclusion: Study results raise the importance of interventional educational measures to promote healthcare professionals’ knowledge of the human microbiome and their potential beneficence on pharmacists’ attitudes and practices regarding antibiotics and probiotics dispensing. The results also denote the urgent need for probiotics’ clinical guidelines to ensure practice uniformity.Keywords: human microbiome, antibiotics, probiotics

Abstract The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and information sharing among consortium members, which includes collaborators in academia and industry. The 2023 annual symposium was a hybrid meeting held in Washington DC on 26–27 September 2023 concurrent with the virtual attendance, with oral and poster presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) Environmental Microbiome Characterization; 2) Microbiome Analysis; 3) Human Microbiome Characterization; 4) Microbiome Engineering; and 5) In Vitro and In Vivo Microbiome Models. Collectively, the symposium provided an update on the scope of current DoD and DoD-affiliated microbiome research efforts and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 7th annual TSMC symposium.

In recent years, a vast array of thinkers have been invested in challenging the long-standing binary division between the human and nonhuman. The notion of the human microbiome especially attests to the truth of such a complication, since current research in biology strongly suggests that we are at the very least as much microbe as we are human and that the number of microorganisms in the human body outnumber distinctly human cells considerably. In this article, we aim to bring the biological notion of the human microbiome in dialogue with Object-Oriented Ontology (OOO) so as to ultimately show that there can be a fruitful exchange of ideas between the two currents of microbiome research and OOO more specifically, and that Graham Harman’s top-down account of objective emergence can be fruitfully a bottom-up approach according to which the parts of an object also impact and constrain the whole.

Abstract In human microbiome studies, mediation analysis has recently been spotlighted as a practical and powerful analytic tool to survey the causal roles of the microbiome as a mediator to explain the observed relationships between a medical treatment/environmental exposure and a human disease. We also note that, in a clinical research, investigators often trace disease progression sequentially in time; as such, time-to-event (e.g., time-to-disease, time-to-cure) responses, known as survival responses, are prevalent as a surrogate variable for human health or disease. In this paper, we introduce a web cloud computing platform, named as microbiome mediation analysis with survival responses (MiMedSurv), for comprehensive microbiome mediation analysis with survival responses on user-friendly web environments. MiMedSurv is an extension of our prior web cloud computing platform, named as microbiome mediation analysis (MiMed), for survival responses. The two main features that are well-distinguished are as follows. First, MiMedSurv conducts some baseline exploratory non-mediational survival analysis, not involving microbiome, to survey the disparity in survival response between medical treatments/environmental exposures. Then, MiMedSurv identifies the mediating roles of the microbiome in various aspects: (i) as a microbial ecosystem using ecological indices (e.g., alpha and beta diversity indices) and (ii) as individual microbial taxa in various hierarchies (e.g., phyla, classes, orders, families, genera, species). To illustrate its use, we survey the mediating roles of the gut microbiome between antibiotic treatment and time-to-type 1 diabetes. MiMedSurv is freely available on our web server ( http://mimedsurv.micloud.kr ).

Background: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated. Methods: In this case–control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation–maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls. Results: The α-diversity of dust microorganisms in AR was lower than that in control group (P = 0.034), and the β-diversity indices of microorganisms in nasal cavity (P = 0.020), skin (P = 0.001) and dust (P = 0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score > 2, P < 0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P < 0.05). The same significantly higher transfer proportions(P < 0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC = 0.88) followed by nasal(AUC = 0.81) and dermal ones(AUC = 0.80). Conclusions: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children. [ABSTRACT FROM AUTHOR]

Background: The rapid establishment and persistence of latent HIV-1 reservoirs is one of the main obstacles towards an HIV cure. While antiretroviral therapy supresses viral replication, it does not eradicate the latent reservoir of HIV-1-infected cells. Recent evidence suggests that the human microbiome, particularly the gut microbiome, may have the potential to modulate the HIV-1 reservoir. However, literature is limited and the exact mechanisms underlying the role of the microbiome in HIV immunity and potential regulation of the viral reservoir remain poorly understood. Results: Here, we review updated knowledge on the associations between the human microbiome and HIV reservoir across different anatomical sites, including the gut, the lungs and blood. We provide an overview of the predominant taxa associated with prominent microbiome changes in the context of HIV infection. Based on the current evidence, we summarize the main study findings, with specific focus on consistent bacterial and related byproduct associations. Specifically, we address the contribution of immune activation and inflammatory signatures on HIV-1 persistence. Furthermore, we discuss possible scenarios by which bacterial-associated inflammatory mediators, related metabolites and host immune signatures may modulate the HIV reservoir size. Finally, we speculate on potential implications of microbiome-based therapeutics for future HIV-1 cure strategies, highlighting challenges and limitations inherent in this research field. Conclusions: Despite recent advances, this review underscores the need for further research to deepen the understanding of the complex interplay between the human microbiome and HIV reservoir. Further integrative multi-omics assessments and functional studies are crucial to test the outlined hypothesis and to identify potential therapeutic targets ultimately able to achieve an effective cure for HIV. [ABSTRACT FROM AUTHOR]

Investigating microbe–microbe interactions at the single-cell level is critical to unraveling the ecology and dynamics of microbial communities. In many situations, microbes assemble themselves into densely packed multispecies biofilms. The density and complexity pose acute difficulties for visualizing individual cells and analyzing their interactions. Here, we address this problem through an unconventional application of expansion microscopy, which allows for the “decrowding” of individual bacterial cells within a multispecies community. Expansion microscopy generally has been carried out under isotropic expansion conditions and used as a resolution-enhancing method. In our variation of expansion microscopy, we carry out expansion under heterotropic conditions; that is, we expand the space between bacterial cells but not the space within individual cells. The separation of individual bacterial cells from each other reflects the competition between the expansion force pulling them apart and the adhesion force holding them together. We employed heterotropic expansion microscopy to study the relative strength of adhesion in model biofilm communities. These included mono- and dual-species Streptococcus biofilms and a three-species synthetic community (Fusobacterium nucleatum, Streptococcus mutans, and Streptococcus sanguinis) under conditions that facilitated interspecies coaggregation. Using adhesion mutants, we investigated the interplay between F. nucleatum outer membrane protein RadD and different Streptococcus species. We also examined the Schaalia-TM7 epibiont association. Quantitative proximity analysis was used to evaluate the separation of individual microbial members. Our study demonstrates that heterotropic expansion microscopy can “decrowd” dense biofilm communities, improve visualization of individual bacterial members, and enable analysis of microbe–microbe adhesive interactions at the single-cell level. [ABSTRACT FROM AUTHOR]

Here, we describe "obelisks," a class of heritable RNA elements sharing several properties: (1) apparently circular RNA ∼1 kb genome assemblies, (2) predicted rod-like genome-wide secondary structures, and (3) open reading frames encoding a novel "Oblin" protein superfamily. A subset of obelisks includes a variant hammerhead self-cleaving ribozyme. Obelisks form their own phylogenetic group without detectable similarity to known biological agents. Surveying globally, we identified 29,959 distinct obelisks (clustered at 90% sequence identity) from diverse ecological niches. Obelisks are prevalent in human microbiomes, with detection in ∼7% (29/440) and ∼50% (17/32) of queried stool and oral metatranscriptomes, respectively. We establish Streptococcus sanguinis as a cellular host of a specific obelisk and find that this obelisk's maintenance is not essential for bacterial growth. Our observations identify obelisks as a class of diverse RNAs of yet-to-be-determined impact that have colonized and gone unnoticed in human and global microbiomes. [Display omitted] • Obelisks are a phylogenetically distinct group of microbiome-associated, viroid-like RNAs • Found globally in diverse niches, obelisks also occur in human stool and oral microbiomes • The human oral bacterium Streptococcus sanguinis SK36 harbors a distinct "obelisk- S.s " • Under replete growth conditions, obelisk- S.s appears to be disposable for SK36 growth Obelisks are widespread RNA-based agents found in diverse environmental and human-associated microbiomes. These apparently unbranched and circular RNAs represent a previously uncharacterized class of genetic elements. [ABSTRACT FROM AUTHOR]

Introduction: Although the oral cavity and the gut are anatomically continuous regions of the gastrointestinal tract, research on the relationship between oral and gut microbiota remains sparse. Oral-gut bacterial translocation is mostly studied in pathological contexts, thus evidence of translocation in healthy conditions is still scarce. Studying the oral-gut microbiota relationship in humans in different life stages is necessary in order to understand how these microbial communities might relate throughout life. Methods: In this study, saliva and fecal samples were collected from healthy participants (39 children, 97 adults). Microbiota analysis was carried out by sequencing the V4 region of the 16S ribosomal RNA gene, followed by amplicon sequence variant (ASV) analysis. Results and discussion: Although the oral and gut microbiota are vastly different, a subset of 61 ASVs were present in both the oral cavity and gut of the same individual, and represented 1.6% of all ASVs detected. From these, 26 ASVs (classified into 18 genera: Actinomyces , Rothia , Bacteroides , Porphyromonas , Prevotella , Alistipes , Fusobacterium , Neisseria , Haemophilus , Akkermansia , Solobacterium , Granulicatella , Streptococcus , Gemella , Mogibacterium , Dialister , Veillonella , Christensenellaceae R-7 group) were present in both children and adults, suggesting the possibility of persistent colonization of both habitats by these microorganisms, initiating in childhood. Additionally, 62% of shared ASVs were more abundant in the oral cavity, indicating that oral-to-gut translocation may be the main route of translocation between environments, and highlighting that this phenomenon might be more common than previously thought in healthy individuals of all ages. [ABSTRACT FROM AUTHOR]

The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and information sharing among consortium members, which includes collaborators in academia and industry. The 2023 annual symposium was a hybrid meeting held in Washington DC on 26–27 September 2023 concurrent with the virtual attendance, with oral and poster presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) Environmental Microbiome Characterization; 2) Microbiome Analysis; 3) Human Microbiome Characterization; 4) Microbiome Engineering; and 5) In Vitro and In Vivo Microbiome Models. Collectively, the symposium provided an update on the scope of current DoD and DoD-affiliated microbiome research efforts and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 7th annual TSMC symposium. [ABSTRACT FROM AUTHOR]

Introduction: Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites. Methods: CHAMP uses a reference database derived from 30,382 human microbiome samples, covering 6,567 prokaryotic and 244 eukaryotic species, as well as 64,003 viruses. We benchmarked CHAMP against established profiling tools (MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta) using a diverse set of in silico metagenomes and DNA mock communities. Results: CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. The false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than other tools at low sequencing depths, highlighting its application for low biomass samples. Discussion: Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. [ABSTRACT FROM AUTHOR]

Follicular skin disorders, including hidradenitis suppurativa (HS), frequently coexist with systemic autoinflammatory diseases, such as inflammatory bowel disease (IBD) and its subtypes, Crohn's disease and ulcerative colitis. Previous studies suggest that dysbiosis of the human gut microbiome may serve as a pathogenic link between HS and IBD. However, the role of the microbiome (gut, skin, and blood) in the context of IBD and various follicular disorders remains underexplored. Here, we performed a systematic review to investigate the relationship between follicular skin disorders, IBD, and the microbiome. Of the sixteen included studies, four evaluated the impact of diet on the microbiome in HS patients, highlighting a possible link between gut dysbiosis and yeast-exclusion diets. Ten studies explored bacterial colonization and HS severity with specific gut and skin microbiota, including Enterococcus and Veillonella. Two studies reported on immunological or serological biomarkers in HS patients with autoinflammatory disease, including IBD, and identified common markers including elevated cytokines and T-lymphocytes. Six studies investigated HS and IBD patients concurrently. Our systematic literature review highlights the complex interplay between the human microbiome, IBD, and follicular disorders with a particular focus on HS. The results indicate that dietary modifications hold promise as a therapeutic intervention to mitigate the burden of HS and IBD. Microbiota analyses and the identification of key serological biomarkers are crucial for a deeper understanding of the impact of dysbiosis in these conditions. Future research is needed to more thoroughly delineate the causal versus associative roles of dysbiosis in patients with both follicular disorders and IBD. [ABSTRACT FROM AUTHOR]

Background: Green tea kombucha (GTK) is a fermented beverage with promising health benefits, but few studies proved its impact on human health. Thus, we aimed to investigate the impact of GTK on weight loss, inflammation, and salivary microbiota in individuals with excess body weight. Methods: This is a randomized controlled clinical trial that lasted 10 weeks with two groups of individuals with excess body weight: control (CG; n = 29; caloric restriction) and kombucha (KG; n = 30; caloric restriction + 200 mL GTK). Body composition, anthropometry, saliva, and blood collection were performed in the beginning and end of the intervention. Plasma interleukins were determined by flow cytometry. Salivary microbiota was analyzed by 16S rRNA sequencing. Results: Both groups decreased weight, BMI, and body fat (p < 0.001) after the intervention, but there were no differences between groups. The KG reduced lipid accumulation product (LAP) (p = 0.029). Both groups decreased IL-1β and IL-8, but IL-6 increased in the CG (p = 0.023) compared to the kombucha group. Alpha and beta diversity of salivary microbiota increased in the KG. Moreover, the KG presented lower Bacillota/Bacteroidota ratio (p = 0.028), and BMI was positively associated with the Bacillota phylum. Conclusions: GTK did not enhance weight loss, but it decreased the LAP. GTK helped in the inflammatory profile and induced positive changes in oral microbiota composition. [ABSTRACT FROM AUTHOR]

Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such community--the human dental plaque biofilm--a network of filamentous Corynebacterium matruchotii cells forms the core of bacterial consortia known as hedgehogs, but the processes that generate these structures are unclear. Here, using live-cell time-lapse microscopy and fluorescent D-amino acids to track peptidoglycan biosynthesis, we report an extraordinary example of simultaneous multiple division within the domain Bacteria. We show that C. matruchotii cells elongate at one pole through tip extension, similar to the growth strategy of soil-dwelling Streptomyces bacteria. Filaments elongate rapidly, at rates more than five times greater than other closely related bacterial species. Following elongation, many septa form simultaneously, and each cell divides into 3 to 14 daughter cells, depending on the length of the mother filament. The daughter cells then nucleate outgrowth of new thinner vegetative filaments, generating the classic "whip handle" morphology of this taxon. Our results expand the known diversity of bacterial cell cycles and help explain how this filamentous bacterium can compete for space, access nutrients, and form important interspecies interactions within dental plaque. [ABSTRACT FROM AUTHOR]

Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals. [ABSTRACT FROM AUTHOR]

In human microbiome studies, mediation analysis has recently been spotlighted as a practical and powerful analytic tool to survey the causal roles of the microbiome as a mediator to explain the observed relationships between a medical treatment/environmental exposure and a human disease. We also note that, in a clinical research, investigators often trace disease progression sequentially in time; as such, time-to-event (e.g., time-to-disease, time-to-cure) responses, known as survival responses, are prevalent as a surrogate variable for human health or disease. In this paper, we introduce a web cloud computing platform, named as microbiome mediation analysis with survival responses (MiMedSurv), for comprehensive microbiome mediation analysis with survival responses on user-friendly web environments. MiMedSurv is an extension of our prior web cloud computing platform, named as microbiome mediation analysis (MiMed), for survival responses. The two main features that are well-distinguished are as follows. First, MiMedSurv conducts some baseline exploratory non-mediational survival analysis, not involving microbiome, to survey the disparity in survival response between medical treatments/environmental exposures. Then, MiMedSurv identifies the mediating roles of the microbiome in various aspects: (i) as a microbial ecosystem using ecological indices (e.g., alpha and beta diversity indices) and (ii) as individual microbial taxa in various hierarchies (e.g., phyla, classes, orders, families, genera, species). To illustrate its use, we survey the mediating roles of the gut microbiome between antibiotic treatment and time-to-type 1 diabetes. MiMedSurv is freely available on our web server (http://mimedsurv.micloud.kr). [ABSTRACT FROM AUTHOR]

ABSTRACT Considering that the human microbiota plays a critical role in health and disease, an accurate and high-resolution taxonomic classification is thus essential for meaningful microbiome analysis. In this study, we developed an automatic system, named MultiTax pipeline, for generating de novo taxonomy from full-length 16S rRNA sequences using the Genome Taxonomy Database and other existing reference databases. We first constructed the MultiTax-human database, a high-resolution resource specifically designed for human microbiome research and clinical applications. The database includes 842,649 high-quality full-length 16S rRNA sequences, extracted from multiple public repositories and human-related studies, offering a comprehensive and accurate portrayal of the human microbiome. To validate the MultiTax-human database, we profiled the human microbiome across various body sites, identified core microbial taxa, and tested its performance using an independent data set. Additionally, the database is equipped with a user-friendly web interface for easy querying and data exploration. The MultiTax-human database is poised to serve as a valuable tool for researchers, enhancing the precision of human microbiome studies and advancing our understanding of its impact on human health and diseases.IMPORTANCEUnderstanding the human microbiome, the collection of microorganisms in and on our bodies, is essential for advancing health research. Current methods often lack precision and consistency, hindering our ability to study these microorganisms effectively. Our study presents the MultiTax-human database, a high-resolution reference tool specifically designed for human microbiome research. By integrating data from multiple sources and employing advanced classification techniques, this database offers an accurate and detailed map of the human microbiome. This resource enhances the ability of researchers and clinicians to explore the roles of microorganisms in health and disease, potentially leading to improved diagnostics, treatments, and insights into various medical conditions.

ABSTRACT The concept of genome–microbiome interactions, in which the microenvironment determined by host genetic polymorphisms regulates the local microbiota, is important in the pathogenesis of human disease. In otolaryngology, the resident bacterial microbiota is reportedly altered in non-infectious ear diseases, such as otitis media pearls and exudative otitis media. We hypothesized that a single-nucleotide polymorphism in the ATP-binding cassette sub-family C member 11 (ABCC11) gene, which determines earwax properties, regulates the ear canal microbiota. We analyzed ABCC11 gene polymorphisms and ear canal microbiota in healthy individuals to understand the relationship between genome–microbiome interactions in the ear canal. The study included 21 subjects who were divided into two groups: 538GA (9) and 538AA (12). Staphylococcus auricularis and Corynebacterium spp. were observed in the 538GA group, whereas Methylocella spp. was observed in the 538AA group. PICRUSt analysis revealed significant enrichment of certain pathways, such as superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation, chlorosalicylate degradation, mycothiol biosynthesis, and enterobactin biosynthesis in the GA group, whereas allantoin degradation IV (anaerobic), nitrifier denitrification, starch degradation III, L-valine degradation I, and nicotinate degradation I were significantly enriched in the AA group. The ABCC11 gene polymorphism regulates the composition of the ear canal microbiota and its metabolic pathways. This study revealed a genome–microbiome interaction within the resident microbiota of the external auditory canal that may help to elucidate the pathogenesis of ear diseases and develop novel therapies.IMPORTANCEThe ABCC11 gene polymorphism, which determines earwax characteristics, regulates the composition of the ear canal microbiota and its metabolic pathways. We determined the presence of genome–microbiome interactions in the resident microbiota of the ear canal. Future studies should focus on ABCC11 gene polymorphisms to elucidate the pathogenesis of ear diseases and develop therapeutic methods.

ABSTRACT Mediation analysis has emerged as a versatile tool for answering mechanistic questions in microbiome research because it provides a statistical framework for attributing treatment effects to alternative causal pathways. Using a series of linked regressions, this analysis quantifies how complementary data relate to one another and respond to treatments. Despite these advances, existing software’s rigid assumptions often result in users viewing mediation analysis as a black box. We designed the multimedia R package to make advanced mediation analysis techniques accessible, ensuring that statistical components are interpretable and adaptable. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis, enabling experimentation with various mediator and outcome models while maintaining a simple overall workflow. The software includes modules for regularized linear, compositional, random forest, hierarchical, and hurdle modeling, making it well-suited to microbiome data. We illustrate the package through two case studies. The first re-analyzes a study of the microbiome and metabolome of Inflammatory Bowel Disease patients, uncovering potential mechanistic interactions between the microbiome and disease-associated metabolites, not found in the original study. The second analyzes new data about the influence of mindfulness practice on the microbiome. The mediation analysis highlights shifts in taxa previously associated with depression that cannot be explained indirectly by diet or sleep behaviors alone. A gallery of examples and further documentation can be found at https://go.wisc.edu/830110.IMPORTANCEMicrobiome studies routinely gather complementary data to capture different aspects of a microbiome’s response to a change, such as the introduction of a therapeutic. Mediation analysis clarifies the extent to which responses occur sequentially via mediators, thereby supporting causal, rather than purely descriptive, interpretation. Multimedia is a modular R package with close ties to the wider microbiome software ecosystem that makes statistically rigorous, flexible mediation analysis easily accessible, setting the stage for precise and causally informed microbiome engineering.

The interactions between macronutrients, the human gut microbiome, and their metabolites (short-chain fatty acids) were comprehensively investigated via an in vitro digestion and fermentation model subjected to eight pulse species. 16S rRNA sequencing and taxonomic analysis of pulse digesta fermented for up to 24 h revealed an increase in the relative abundance of gut health-detrimental genera represented by Escherichia-Shigella in kidney bean, soybean, cowpea, chickpea, and black bean samples. In contrast, the relative abundance of health-positive genera, including Bacteroides, Eubacterium, and Akkermansia, was elevated in red bean, mung bean, and Heunguseul. At the same time, the proportion of the pathogenic Escherichia-Shigella decreased. Concurrently, these three species exhibited an increase in microbial diversity as evidenced by the calculation of α-diversity (Shannon index) and β-diversity (Bray-Curtis distance). Despite the lower nutrient contents in the three pulses, represented by carbohydrates, amino acids, and fatty acids, network analysis revealed that the nutrient contents in the pulse digesta possess complex positive or negative correlations with a variety of bacteria, as well as their metabolites. These correlations were more pronounced in red bean, mung bean, and Heunguseul than in the other pulses. It was postulated that the overall potential to nourish gut environments in these species was due to the balance of their nutritional components. The linear regression analysis demonstrated that there was a negative association between carbohydrate and amino acid contents and the increase in Shannon indices. Furthermore, the ratio of carbohydrates to fatty acids and amino acids to fatty acids displayed negative correlations with the diversity increase. The ratio of carbohydrates to amino acids showed a weak positive correlation. It is noteworthy that a diet comprising foods with a balanced nutritional profile supports the growth of beneficial gut microbes, thereby promoting microbial eubiosis. Consistent work on different ingredients is essential for precise insight into the interplay between food and the human microbiome in complex dietary patterns.

ABSTRACT The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographic regions. In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). The analysis revealed significant differences in microbial communities among the four regions. Cutibacterium was the most abundant bacterium in palmar samples from Shanghai and Kunming, Psychrobacter in Chifeng samples, and Psychrobacillus in Urumqi samples. Additionally, Streptococcus and Staphylococcus were the dominant bacteria in the oral and nasal cavities. Individuals from the four regions could be distinguished and predicted based on a model constructed using the random forest algorithm, with the predictive effect of palmar microbiota being better than that of oral and nasal cavities. The prediction accuracy using hypervariable regions (V3-V4 and V4-V5) was comparable with that of using the entire 16S rRNA. Overall, our study highlights the distinctiveness of the human microbiome in individuals living in these four regions. Furthermore, the microbiome can serve as a biomarker for geographic origin inference, which has immense application value in forensic science.IMPORTANCEMicrobial communities in human hosts play a significant role in health and disease, varying in species, quantity, and composition due to factors such as gender, ethnicity, health status, lifestyle, and living environment. The characteristics of microbial composition at various body sites of individuals from different regions remain largely unexplored. This study utilized single-molecule real-time sequencing technology to detect the entire 16S rRNA gene of bacteria residing in the palmar skin, oral, and nasal cavities of Han individuals from four regions in China. The composition and structure of the bacteria at these three body sites were well characterized and found to differ regionally. The results elucidate the differences in bacterial communities colonizing these body sites across different regions and reveal the influence of geographical factors on human bacteria. These findings not only contribute to a deeper understanding of the diversity and geographical distribution of human bacteria but also enrich the microbiome data of the Asian population for further studies.

The human body harbors an extremely complex and dynamic microbial community (10-100 trillion) of bacteria, archaea, viruses, and eukaryotes. The human microbiota plays a crucial role in the environment and human health under normal circumstances; nonetheless, dysfunction of the human microbiome has been associated with illnesses ranging from inflammatory bowel disease to multidrug-resistant infections. Culture-dependent human microbial exploration approaches are inadequate for discovering the diversity, abundance, and full genetic and metabolic potential of the whole microbial ecosystem. Hence, metagenomics analysis is a powerful advanced technology for comprehensively studying human microbial composition and diversity, exploring novel and antibiotic resistance genes, microbial metabolic pathways, functional dysbiosis, and co-evolution of the microbiome with the host. Therefore, owing to the increase in human microbiome sequencing projects in healthy and diseased people worldwide, it is feasible to explore the human microbiome using a metagenomics approach. Thus, this review focuses on the advancement of metagenomics for exploring the human microbiome, human microbiome metagenomics data processing, and analysis strategies. Currently used bioinformatics tools and their approaches are also discussed in the context of human microbial metagenomics.

Archaea represent a separate domain of life, next to bacteria and eukarya. As components of the human microbiome, archaea have been associated with various diseases, including periodontitis, endodontic infections, small intestinal bacterial overgrowth, and urogenital tract infections. Archaea are generally considered nonpathogenic; the reasons are speculative because of limited knowledge and gene annotation challenges. Nevertheless, archaeal syntrophic principles that shape global microbial networks aid both archaea and potentially pathogenic bacteria. Evaluating archaea interactions remains challenging, requiring clinical studies on inflammatory potential and the effects of archaeal metabolism. Establishing a culture collection is crucial for investigating archaea functions within the human microbiome, which could improve health outcomes in infectious diseases. We summarize potential reasons for archaeal nonpathogenicity, assess the association with infectious diseases in humans, and discuss the necessary experimental steps to enable mechanistic studies involving archaea.

Establishing geographical location is a crucial aspect of forensic sciences, distinguishing between primary and secondary crime scenes, linking an individual to a crime scene, or detecting sources of disease. Microorganisms can be used as geolocation indicators since microbial communities vary according to climatic factors (e.g. temperature, humidity, soil properties, altitude). Therefore, this systematic review aimed to investigate whether the human or environmental microbiomes help to determine a crime's geolocation. Articles were searched in PubMed,Scopus and Web of Science using keywords and data fields. The final selection included seven (of 172) manuscripts. The results showed that the microbial profile of either human or environmental samples have the potential to link a cadaver or a crime scene to a given location, highlighting microbes' usefulness in obtaining information from geographical locations (e.g. soil samples from a suspect's shoe matched to a source). However, research is required before applying this forensic strategy to real scenarios. For instance, optimizing and standardizing the microbiome analysis methods and determining several factors that may influence the results. [ABSTRACT FROM AUTHOR]

The use of medicinal plants has increased tremendously and that has led to the scientific interest for testing this plant for toxicity and antimicrobial activity. The manuscript used a comprehensive literature search from databases such as PubMed, Google Scholar, and ScienceDirect to identify relevant studies published within the last five years (2018-2023) and selectively those beyond that provide the necessary background to the article. The literature analysis found a huge scientific progress made and a lot of plants have been tested for safe use and antimicrobial resistance using the different microorganisms. Nonetheless, the article also highlights the possible hormonal effect or microbiota imbalance which could be attributed to these medical plants being used without proper guidance among our population. Age wise on patients, any prolonged use of these medicinal plants may have devastating effects as such this article advocates for a thorough understanding of the normal flora when communities are treated at home by traditional healers. [ABSTRACT FROM AUTHOR]

This paper tried to analyze publications on "Human microbiome," globally over the last 22 years i.e. 2002- 2023 and summarize the most advanced achievements in this field, data retrieved from SCOPUS database. The total 3814 number of research publications found and extracted and further analyzed in selected parameters for fulfillment of the objectives of the study. This research aims to assess the global research productivity on the "Human microbiome." In respect of Literature Publications "United States" is at the top among the world with publications (TP=1858), followed by "China (TP=321)", "United Kingdom (TP=234)", "Germany (TP=216)", "Canada (TP=213)" and "India (TP=183)" in this field during this time. "Frontiers in Microbiology" is the most presiding journal in the field of "Human Microbiome" with 113 publications followed by "Plos One" with 100 publications. We use an open-source tool, VOSviewer for classic logical bibliometric analysis. [ABSTRACT FROM AUTHOR]

Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding betweenmicrobiologists andmodelers/bioinformaticians, stemming froma lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored formicrobiologists, researchers newtomicrobiomemodeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling. [ABSTRACT FROM AUTHOR]

This article reformulates Stephan Helmreich´s the ¨microbiomisation of race¨ as the historiality of otherness in the foundations of human microbiome science. Through the lens of my ethnographic fieldwork of a transnational community of microbiome scientists that conducted a landmark human microbiome research on indigenous microbes and its affiliated and first personalised microbiome initiative, the American Gut Project, I follow and trace the key actors, experimental systems and onto-epistemic claims in the emergence of human microbiome science a decade ago. In doing so, I show the links between the reinscription of race, comparative research on the microbial genetic variation of human populations and the remining of bioprospected data for personalised medicine. In these unpredictable research movements, the microbiome of non-Western peoples and territories is much more than a side project or a specific approach within the field: it constitutes the nucleus of its experimental system, opening towards subsequent and cumulative research processes and knowledge production in human microbiome science. The article demonstrates that while human microbiome science is articulated upon the microbial 'makeup' of non-wester(nised) communities, societies, and locales, its results and therapeutics are only applicable to medical conditions affecting rich nations (i.e., inflammatory, autoimmune, and metabolic diseases). My reformulation of ¨microbiomisation of race¨ as the condition of possibility of human microbiome science reveals that its individual dimension is sustained by microbial DNA data from human populations through bioprospecting practices and gains meaning through personalised medicine initiatives, informal online networks of pseudoscientific and commodified microbial-related evidence. [ABSTRACT FROM AUTHOR]

Different modifications of the standard bread recipe have been proposed to improve its nutritional and health benefits. Here, we utilized the in vitro Human Gut Simulator (HGS) to assess the fermentation of one such artisan bread by human gut microbiota. Dried and milled bread, composed of almond flour, psyllium husks, and flax seeds as its three main ingredients, was first subjected to an in vitro protocol designed to mimic human oro-gastro-intestinal digestion. The bread digest was then supplied to complex human gut microbial communities, replacing the typical Western diet-based medium (WM) of the GHS system. Switching the medium from WM to bread digest resulted in statistically significant alterations in the community structure, encoded functions, produced short-chain fatty acids, and available antioxidants. The abundances of dietary fiber degraders Enterocloster, Mitsuokella, and Prevotella increased; levels of Gemmiger, Faecalibacterium, and Blautia decreased. These community alterations resembled the previously revealed differences in the distal gut microbiota of healthy human subjects consuming typical Mediterranean vs. Western-pattern diets. Therefore, the consumption of bread high in dietary fiber and unsaturated fatty acids might recapitulate the beneficial effects of the Mediterranean diet on the gut microbiota. [ABSTRACT FROM AUTHOR]