The healthy human microbiome

Exploring the role of gut microbiota in antibiotic resistance and prevention

BACKGROUND/INTRODUCTION

Antimicrobial resistance (AMR) and the evolution of multiple drug-resistant (MDR) bacteria is of grave public health concern. To combat the pandemic of AMR, it is necessary to focus on novel alternatives for drug development. Within the host, the interaction of the pathogen with the microbiome plays a pivotal role in determining the outcome of pathogenesis. Therefore, microbiome-pathogen interaction is one of the potential targets to be explored for novel antimicrobials.

MAIN BODY

This review focuses on how the gut microbiome has evolved as a significant component of the resistome as a source of antibiotic resistance genes (ARGs). Antibiotics alter the composition of the native microbiota of the host by favouring resistant bacteria that can manifest as opportunistic infections. Furthermore, gut dysbiosis has also been linked to low-dosage antibiotic ingestion or subtherapeutic antibiotic treatment (STAT) from food and the environment.

DISCUSSION

Colonization by MDR bacteria is potentially acquired and maintained in the gut microbiota. Therefore, it is pivotal to understand microbial diversity and its role in adapting pathogens to AMR. Implementing several strategies to prevent or treat dysbiosis is necessary, including faecal microbiota transplantation, probiotics and prebiotics, phage therapy, drug delivery models, and antimicrobial stewardship regulation.

Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut

In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.

Gut Microbiota: A Modulator and Therapeutic Target for Chronic Pain

Chronic pain is a prevalent condition, impacting nearly one-fifth of the global population. Despite the availability of various clinical treatments, each comes with inherent limitations, and few offer a complete cure, resulting in a significant social and economic burden. Therefore, it is important to determine the pathogenesis and causes of chronic pain. Numerous studies have shown a close link between the intestinal microflora and chronic pain. The gut microbiota can exert their effects on chronic pain through both central and peripheral mechanisms and is able to communicate with the brain through its own components or metabolites. They also can regulate chronic pain by affecting pro- and anti-inflammatory cells. This review is aimed at reviewing the connection between gut flora and different types of chronic pain, including visceral pain, neuropathic pain, inflammatory pain, musculoskeletal pain, migraine, and chronic cancer pain; exploring the central and peripheral mechanisms of the influence of gut flora on chronic pain; and attempting to provide novel treatment options for chronic pain, that is, the gut microbiota can be regulated by probiotics, fecal microbial transplantation, and natural products to treat chronic pain. By examining the intricate relationship between gut flora and chronic pain, the review sought to pave the way for new treatment strategies that target the gut microbiota, offering hope for more effective pain management.

Characteristics of upper and lower respiratory tract microbiota after lung transplantation

BACKGROUND

The composition and characteristics of airway microbiota offer critical insights for clinical decision-making. Current research on chronic lung diseases shows differences in the composition and characteristics of upper and lower respiratory tract microbiota compared with healthy individuals. However, the temporal changes of these microbial communities in lung transplant recipients remain poorly characterized.

METHODS

This is a longitudinal prospective study. Respiratory specimens were collected regularly from lung transplant recipients for testing and analysis. A total of 150 bronchoalveolar lavage fluid (BALF) samples, 150 throat swab samples, 51 sputum samples, and 36 lung tissue samples were collected from the recipients, at 7 days, 14 days, 1 month, 2 months, 3 months, and 6 months post-transplant for 16S rRNA gene sequencing and analysis.

RESULTS

Our study showed that there were significant differences in α-diversity and β-diversity among lung tissue, throat swab, and sputum samples, although α-diversity did not show a significant difference between lung tissue and BALF. Most amplicon sequence variants (ASVs) belonged to the families Enterobacteriaceae, Pseudomonadaceae, and Stenotrophomonas in BALF, while most ASVs belonged to the genera Streptococcus, Pseudomonadaceae, and Stenotrophomonas in sputum samples. Regarding dynamic changes, Corynebacterium and Staphylococcus were more prevalent in the early post-operative period but gradually decreased by 7 days post-operatively, while the common microbiota found in healthy populations based on literature became the most abundant ASVs at 6 months post-operatively in our study participants. Pseudomonadaceae and Stenotrophomonas contributed to the similarity in the composition of upper and lower respiratory microbiota.

CONCLUSIONS

This study demonstrates that lung transplant recipients exhibit unique characteristics in their upper and lower respiratory tract microbiota, which are distinct ecological profiles, and both undergo significant changes within 6 months post-operatively. The similarity between upper and lower respiratory tract microbiota is associated with microbial diversity and taxonomic dominance.

CLINICAL TRIAL

The clinical trial was registered at Chinese Clinical Trial Registry (ChiCTR2200056908) in February 2022.

The Use of Biomarkers in Precision Health Symptom Science-Opportunities and Challenges

OBJECTIVES

Precision health symptom science applies person-centered approaches to elucidate interindividual differences in patients' symptom experiences and incorporates omics methods with social, societal, and environmental determinants of health to develop symptom management strategies. By filling scientific gaps related to patients' symptom experiences and their underlying mechanisms, interventions can be developed to improve quality of life and outcomes. The purposes of this article are to describe symptom phenotype development; review analytical approaches to identify a symptom phenotype; and discuss common and emerging methods for biomarker discovery and their implications in precision health symptom science.

METHODS

Peer-reviewed research studies, review articles, and scientific expertise were synthesized to provide a broad overview of several methods of biomarker discovery and their implications for precision health symptom science.

RESULTS

Approaches to symptom phenotype development and analytical methods for phenotype identification were reviewed. Common (ie, genomic, epigenomic, transcriptomic, proteomic, metabolomic, microbiome) and emerging (ie, polygenic risk scores, microRNA, epigenetic clocks, allostatic load, wearables) methods for biomarker discovery were described. Each method provides unique information to improve our understanding of the complex biological processes that underlie symptoms and may be used for risk prediction, screening, surveillance, and treatment response.

CONCLUSIONS

While the exemplar approaches to conducting precision health symptom science were shared through an oncology lens, they are generalizable across acute and chronic conditions.

IMPLICATIONS FOR NURSING PRACTICE

Symptom biomarker identification is inherently complex and the methods for biomarker collection, processing, measurement, and analysis are continually evolving. Therefore, symptom scientists need to form transdisciplinary teams with experts in omics methodologies and bioinformatics. Despite the challenges, symptom scientists are well suited to lead the way in precision health symptom science to reduce symptom burden and improve quality of life among patients with various chronic conditions.

Similarity of drug targets to human microbiome metaproteome promotes pharmacological promiscuity

Similarity between candidate drug targets and human proteins is commonly assessed to minimize the occurrence of side effects. Although numerous drugs have been found to disrupt the health of the human microbiome, no comprehensive comparison between established drug targets and the human microbiome metaproteome has yet been conducted. Therefore, herein, sequence and structure alignments between human and pathogen drug targets and representative human gut, oral, and vaginal microbiome metaproteomes were performed. Both human and pathogen drug targets were found to be similar in sequence, function, structure, and drug binding capacity to proteins in diverse pathogenic and non-pathogenic bacteria from all three microbiomes. The gut metaproteome was identified as particularly susceptible overall to off-target effects. Certain symptoms, such as infections and immune disorders, may be more common among drugs that non-selectively target host microbiota. These findings suggest that similarities between human microbiome metaproteomes and drug target candidates should be routinely checked.

Preliminary analysis of salivary microbiota in catathrenia (nocturnal groaning) using machine learning algorithms

Objectives

The present study aimed to characterize the salivary microbiota in patients with catathrenia and to longitudinally validate potential biomarkers after treatment with mandibular advancement devices (MAD).

Materials and methods

Twenty-two patients with catathrenia (12 M/10 F, median age 28 y) and 22 age-matched control volunteers (8 M/14 F, median age 30 y) were included in the cross-sectional study. Video/audio polysomnography was conducted for diagnosis. All patients received treatment with custom-fit MAD and were followed for one month. Ten patients (6 M/4 F) underwent post-treatment PSG. Salivary samples were collected, and microbial characteristics were analyzed using 16S rRNA gene sequencing. The 10-fold cross-validated XGBoost and nested Random Forest Classifier machine learning algorithms were utilized to identify potential biomarkers.

Results

In the cross-sectional study, patients with catathrenia had lower α-diversity represented by Chao 1, Faith's phylogenetic diversity (pd), and observed species. Beta-diversity based on the Bray-Curtis dissimilarities revealed a significant inter-group separation (p = 0.001). The inter-group microbiota distribution was significantly different on the phylum and family levels. The treatment of MAD did not alter salivary microbiota distribution significantly. Among the most important genera in catathrenia and control classification identified by machine learning algorithms, four genera, Alloprevotella, Peptostreptococcaceae_XI_G1, Actinomyces and Rothia, changed significantly with MAD treatment. Correlation analysis revealed that Alloprevotella was negatively related to the severity of catathrenia (r2= -0.63, p < 0.001).

Conclusions

High-throughput sequencing revealed that the salivary microbiota composition was significantly altered in patients with catathrenia. Some characteristic genera (Alloprevotella, Peptostreptococcaceae_XI_G1, Actinomyces, and Rothia) could be potential biomarkers sensitive to treatment. Future studies are needed to confirm and determine the mechanisms underlying these findings.

Integrating traditional omics and machine learning approaches to identify microbial biomarkers and therapeutic targets in pediatric inflammatory bowel disease

Background

Pediatric inflammatory bowel disease (IBD), especially Crohn's disease, significantly affects gut health and quality of life. Although gut microbiome research has advanced, identifying reliable biomarkers remains difficult due to microbial complexity.

Methods

We used RNA-seq-based microbial profiling and machine learning (ML) to find robust biomarkers in pediatric IBD. Microbial taxa were profiled at phylum, genus, and species levels using kraken2 on Crohn's disease and non-IBD ileal biopsies. We performed abundance-based analyses and applied four ML models (Logistic Regression, Random Forest, Support Vector Machine, XGBoost) to detect discriminative taxa. An independent cohort of 36 pediatric stool samples assessed by 16S rRNA sequencing validated top ML results.

Results

Traditional abundance-based methods showed compositional shifts but identified few consistently significant taxa. ML models had better discriminatory performance, with XGBoost outperforming others and pinpointing Orthotospovirus and Vescimonas as key genera. These findings were confirmed in the validation cohort, where only one traditionally noted genus, Actinomyces, maintained significance.

Discussion

Integrating conventional omics with AI-driven analytics boosts reproducibility and clinical relevance of microbial biomarker discovery, opening new possibilities for targeted therapies and precision medicine in pediatric IBD.

Fast Encapsulation of Microbes into Dissolvable Hydrogel Beads Enables High-Throughput Microbial Single-Cell RNA Sequencing of Clinical Microbiome Samples

Microbial single-cell RNA-seq (mscRNA-seq) can achieve resolution at the cellular level, enhancing the understanding of microbial communities. However, current high-throughput mscRNA-seq methods are limited by multiple centrifugation steps, which can lead to microbial loss and bias. smGel-seq is reported, a high-throughput single-microbe RNA sequencing method for clinical microbiome samples that employs hydrogel beads to encapsulate individual microbes to reduce microbial loss and input requirements. In this method, a novel microchannel array device is implemented for encapsulating single microbe in dissolvable hydrogel beads (smDHBs), along with an optimized automated microfluidic platform to co-encapsulate barcoded beads and smDHBs, enabling high-throughput barcoding of individual microbes. smGel-seq significantly increases the microbial recovery rate in a gut microbiome sample from 8.8% to 91.8%. Furthermore, this method successfully processes clinical microbiome samples with microbial inputs 20 times lower than those required by previous methods. Notably, smGel-seq enables the first mscRNA-seq in a clinical sputum microbiome sample, revealing a specific microbial subpopulation that may play a key role in environmental adaptability, antibiotic resistance, and pathogenicity. These results highlight the compatibility of smGel-seq with clinical microbiome samples and demonstrate its potential for widespread application in diverse clinical and research settings.

MetaDAVis: An R shiny application for metagenomic data analysis and visualization

The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shiny application. MetaDAVis can perform six different types of analyses that include: i) Taxonomic abundance distribution; ii) Alpha and beta diversity analyses; iii) Dimension reduction tasks using PCA, t-SNE, and UMAP; iv) Correlation analysis using taxa- or sample-based data; v) Heatmap generation; and vi) Differential abundance analysis. MetaDAVis creates interactive and dynamic figures and tables from multiple methods enabling users to easily understand their data using different variables. Our program is user-friendly and easily customizable allowing those without any programming background to perform comprehensive data analyses using a standalone or web-based interface.

Age-related dynamics of predominant methanogenic archaea in the human gut microbiome

BACKGROUND

The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.

METHODS

Shotgun metagenomic data from the stool samples of young adults (n = 127, Age: 19-59 y), older adults (n = 86, Age: 60-99 y), and centenarians (n = 34, age: 100-109 years) were analyzed.

RESULTS

Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.

CONCLUSIONS

This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.

Microbiome alterations in primary Sjögren's syndrome: Regional dysbiosis and microbiome-targeted therapeutic strategies

Primary Sjögren's syndrome (pSS) is a complex autoimmune disease characterized by diverse clinical manifestations. While xerophthalmia and xerostomia are hallmark symptoms, the disease often involves multiple organ systems, including the kidneys, lungs, nervous system, and gastrointestinal tract, leading to systemic morbidity in severe cases. Despite extensive research, the precise pathogenesis of pSS remains unclear, likely involving infectious, hormonal, and genetic factors. Emerging evidence highlights the microbiome as a key contributor to autoimmune diseases, including pSS. Dysbiosis in the oral, ocular, gut, and genital microbiomes plays a critical role in disease onset, progression, and variability. This review summarizes current findings on microbiome alterations in pSS, emphasizing their role in pathogenesis and clinical features, and explores microbiome-targeted therapies. Understanding the role of the microbiome in pSS pathophysiology could advance disease management and inspire targeted therapeutic strategies.

Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives

The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.

Incorporating microbiome analyses can enhance conservation of threatened species and ecosystem functions

Conservation genomics is a rapidly growing subdiscipline of conservation biology that uses genome-wide information to inform management of biodiversity at all levels. Such efforts typically focus on species or systems of conservation interest, but rarely consider associated microbes. At least three major approaches have been used to study how microorganisms broadly contribute to conservation areas: (1) diversity surveys map out microbial species distribution patterns in a variety of hosts, natural environments or regions; (2) functional surveys associate microbial communities with factors of interest, such as host health, symbiotic interactions, environmental characteristics, ecosystem processes, and biological invasions; and (3) manipulative experiments examine the response of changes to microbial communities or determine the functional roles of specific microbes within hosts or communities by adding, removing, or genetically modifying microbes. In practice, multiple approaches are often applied simultaneously. The results from all three conservation genomics approaches can be used to help design practical interventions and improve management actions, some of which we highlight below. However, experimental manipulations allow for more robust causal inferences and should be the ultimate goal of future work. Here we discuss how further integration of microbial research of a host's microbiome and of free living microbes into conservation biology will be an essential advancement for conservation of charismatic organisms and ecosystem functions in light of ongoing global environmental change.

Rapid and accurate testing for urinary tract infection: new clothes for the emperor

SUMMARYUrinary tract infection (UTI) is among the most common infections in clinical practice. In some cases, if left untreated, it can lead to pyelonephritis and urosepsis. In other cases, UTI resolves without treatment. Clinical diagnosis is typically based on patient symptoms and/or urinalysis, including urine dipsticks. The standard urine culture method is sometimes employed to identify the suspected urinary pathogen (uropathogen) and/or guide antimicrobial choice, but results are rarely available before 24 h. The standard urine culture method also misses fastidious, anaerobic, and slow-growing uropathogens and rarely reports polymicrobial infections. The unexplained combination of negative urine cultures with persistent urinary tract symptoms is distressing to both patients and clinicians. Given the broad appreciation of the advantages provided by rapid testing (e.g., for COVID-19 or influenza A), a rapid, accurate diagnostic test is needed to deliver timely treatment to patients seeking care for UTI that optimizes antibiotic stewardship. Herein, we discuss progress being made toward an accessible, timely (i.e., within hours), accurate assay with results that are clinically useful for the treating clinician within the timeframe of the infection (i.e., the growth rate of the pathogen(s)). New and emerging uropathogens often overlooked by current diagnostic techniques are also reviewed.

Cross-validation for training and testing co-occurrence network inference algorithms

BACKGROUND

Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS

Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS

Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.

Tryptophan and Its Metabolite Serotonin Impact Metabolic and Mental Disorders via the Brain-Gut-Microbiome Axis: A Focus on Sex Differences

The crisis of metabolic and mental disorders continues to escalate worldwide. A growing body of research highlights the influence of tryptophan and its metabolites, such as serotonin, beyond their traditional roles in neural signaling. Serotonin acts as a key neurotransmitter within the brain-gut-microbiome axis, a critical bidirectional communication network affecting both metabolism and behavior. Emerging evidence suggests that the gut microbiome regulates brain function and behavior, particularly through microbial influences on tryptophan metabolism and the serotonergic system, both of which are essential for normal functioning. Additionally, sex differences exist in multiple aspects of serotonin-mediated modulation within the brain-gut-microbiome axis, affecting feeding and affective behaviors. This review summarizes the current knowledge from human and animal studies on the influence of tryptophan and its metabolite serotonin on metabolic and behavioral regulation involving the brain and gut microbiome, with a focus on sex differences and the role of sex hormones. We speculate that gut-derived tryptophan and serotonin play essential roles in the pathophysiology that modifies neural circuits, potentially contributing to eating and affective disorders. We propose the gut microbiome as an appealing therapeutic target for metabolic and affective disorders, emphasizing the importance of understanding sex differences in metabolic and behavioral regulation influenced by the brain-gut-microbiome axis. The therapeutic targeting of the gut microbiota and its metabolites may offer a viable strategy for treating serotonin-related disorders, such as eating and affective disorders, with potential differences in treatment efficacy between men and women. This review would promote research on sex differences in metabolic and behavioral regulation impacted by the brain-gut-microbiome axis.

Microbiota shifts in fracture-related infections and pathogenic transitions identified by 16S rDNA sequencing

Fracture-related infection (FRI) is a major challenge in orthopaedic trauma. Understanding of the microbial shift with respect to the initial contamination to infection phase is crucial. This study was to examine the wound microbiota associated with FRI in a prospective cohort study of 155 patients with Gustilo-Anderson Type II, IIIA or IIIB open fractures. Tissue samples were systematically collected from all patients during initial surgical debridement. Out of these, patients who developed infection (FRI group, n = 28) had a second tissue sampling during re-debridement. Conversely, patients who achieved normal healing and subsequently received definitive open reduction and internal fixation served as control (NH group, n = 24). Marked differences between all groups were revealed in the 16S rDNA analysis of microbial communities. The species richness was higher in the Pre-FRI group, but bacterial diversity declined significantly in the FRI group after infection onset. In the Pre-FRI and Pre-NH groups, Firmicutes were the dominating phylum, while in the FRI and NH groups, Proteobacteria and Actinobacteria appeared more prevalent, respectively. In Pre-FRI notably abundant Bacillus and Staphylococcus and in FRI, the most pathogens were Enterobacter and Pseudomonas. The NH group maintained balanced microbial diversity. These findings suggest that declining microbiota diversity and shifts towards dominant pathogens in open fracture patients may serve as early indicators of infection risk, with Bacillus potentially emerging as a predictive biomarker for FRI susceptibility.

Temporary dietary fiber depletion prompts rapid and lasting gut microbiota restructuring in mice

Long-term alterations of the gut microbiota and host symbiosis after a dietary perturbation remain insufficiently understood and characterized. In this study, we investigate the impact of temporary dietary fiber depletion in mice that received a diet with reduced fiber content (RFD) for 3 weeks followed by a return to a standard chow diet for 6 weeks, compared to mice that only received a chow diet. Fiber deprivation was accompanied by a reduction of microbiota diversity and an increase in mucolytic and sulfate-reducing bacteria. The activities of enzymes targeting glycans from the host mucus were increased accordingly, while those targeting plant fibers were decreased. On the host side, we report transiently higher quantities of host DNA in feces during the RFD suggesting an impaired gut barrier function. Six weeks after the return to the chow diet, lasting changes in microbiota composition were observed, as exemplified by the replacement of durably depleted amplicon sequence variants close to Duncaniella dubosii by other members of the Muribaculaceae family. The observation of two distinct gut microbial communities in mice under identical environmental and alimentary conditions at the end of the experiment suggests the existence of alternative stable microbiota states.

IMPORTANCE

In this article, the authors explore the impact of a diet with reduced fiber content on the gut microbiota-host symbiosis in a mouse model. More importantly, they examine the resilience of the intestinal symbiosis after the return to a standard (chow) diet. Some of the measured parameters (intestinal barrier impairment and bacterial glycan-degrading enzymatic activities) returned to control values. However, this was not the case for bacterial richness-the number of different bacteria observed-which remained durably reduced. Among related bacteria, some groups receded and remained undetected until 6 weeks after the return to the chow diet while others saw their abundance increase in replacement. The authors find that a temporary fiber deprivation lasting as little as 3 weeks can cause a transition to an alternative stable microbiota state, i.e., a lasting change in intestinal microbiota composition.

Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans

Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.

Glycaemic sugar metabolism and the gut microbiota: past, present and future

Non-communicable diseases (NCDs), such as type 2 diabetes (T2D) and metabolic dysfunction-associated fatty liver disease, have reached epidemic proportions worldwide. The global increase in dietary sugar consumption, which is largely attributed to the production and widespread use of cheap alternatives such as high-fructose corn syrup, is a major driving factor of NCDs. Therefore, a comprehensive understanding of sugar metabolism and its impact on host health is imperative to rise to the challenge of reducing NCDs. Notably, fructose appears to exert more pronounced deleterious effects than glucose, as hepatic fructose metabolism induces de novo lipogenesis and insulin resistance through distinct mechanisms. Furthermore, recent studies have demonstrated an intricate relationship between sugar metabolism and the small intestinal microbiota (SIM). In contrast to the beneficial role of colonic microbiota in complex carbohydrate metabolism, sugar metabolism by the SIM appears to be less beneficial to the host as it can generate toxic metabolites. These fermentation products can serve as a substrate for fatty acid synthesis, imposing negative health effects on the host. Nevertheless, due to the challenging accessibility of the small intestine, our knowledge of the SIM and its involvement in sugar metabolism remains limited. This review presents an overview of the current knowledge in this field along with implications for future research, ultimately offering potential therapeutic avenues for addressing NCDs.

Mutations in the Staphylococcus aureus Global Regulator CodY confer tolerance to an interspecies redox-active antimicrobial

Bacteria often exist in multispecies communities where interactions among different species can modify individual fitness and behavior. Although many competitive interactions have been described, molecular adaptations that can counter this antagonism and preserve or increase fitness remain underexplored. Here, we characterize the adaptation of Staphylococcus aureus to pyocyanin, a redox-active interspecies antimicrobial produced by Pseudomonas aeruginosa, a co-infecting pathogen frequently isolated from wound and chronic lung infections with S. aureus. Using experimental evolution, we identified mutations in a conserved global transcriptional regulator, CodY, that confer tolerance to pyocyanin and thereby enhance survival of S. aureus. A pyocyanin tolerant CodY mutant also had a survival advantage in co-culture with P. aeruginosa, likely through tolerance specifically to pyocyanin. The transcriptional response of the CodY mutant to pyocyanin indicated a two-pronged defensive response compared to the wild type. First, the CodY mutant strongly suppressed metabolism by downregulating core metabolic pathways , especially translation-associated genes, upon exposure to pyocyanin. Metabolic suppression via ATP depletion was sufficient to provide comparable protection against pyocyanin to the wild-type strain. Second, while both the wild-type and CodY mutant strains upregulated oxidative stress response pathways upon pyocyanin exposure, the CodY mutant overexpressed multiple stress response genes compared to the wild type. We determined that catalase overexpression was critical to pyocyanin tolerance as its absence eliminated tolerance in the CodY mutant and overexpression of catalase was sufficient to impart tolerance to the wild-type strain against purified pyocyanin and in co-culture with WT P. aeruginosa. Together, these results suggest that both transcriptional responses of reduced metabolism and an increased oxidative stress response likely contribute to pyocyanin tolerance in the CodY mutant. Our data thus provide new mechanistic insight into adaptation toward interbacterial antagonism via altered regulation that facilitates multifaceted protective cellular responses.

Microbiome analysis of serum extracellular vesicles in gestational diabetes patients

AIM

Gestational Diabetes Mellitus (GDM) is among the most common complications during pregnancy, posing serious risks to both the patient's and offspring's health and well-being. Alterations in the maternal microbiome are closely associated with the pathogenesis of GDM, with Extracellular Vesicles (EVs) facilitating communication between microbiota and the host. However, little is known about the relationship between the microbial composition within EVs and the pathogenesis of GDM. Therefore, this study aims to characterize the microbiota within serum EVs of GDM Patients (GDM group) and to identify microbial communities that significantly differ from those in Women With Normal Pregnancies (NonGDM group).

METHODS

Blood samples were collected from both groups of patients, and EVs derived from serum were isolated via centrifugation. Identification and characterization of EVs were performed using transmission electron microscopy and nanoparticle flow cytometry. Microbiome analysis of serum EVs from both groups was conducted using 16S rRNA sequencing.

RESULTS

Results indicated altered diversity in microbial communities within serum EVs of GDM patients. Further analysis at the phylum, family, genus, and species levels revealed that Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the dominant taxa in the EVs of both the NonGDM and GDM groups. Specifically, Actinobacteria and Firmicutes showed increased relative abundance in GDM group EVs compared to NonGDM, leading to a higher Firmicutes/Bacteroidetes ratio, while Proteobacteria and Bacteroidetes exhibited decreased relative abundance. Tax4Fun analysis revealed enrichment of microbial functions related to amino acid metabolism, carbohydrate metabolism, energy metabolism, and metabolism of cofactors and vitamins in both patient groups.

CONCLUSION

In conclusion, this study reveals a potential correlation between changes in the microbial composition and diversity of serum EVs and the onset and development of GDM. Furthermore, changes in the relative abundance of Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes may play an important role in the pathogenesis of GDM.

Examining the healthy human microbiome concept

Human microbiomes are essential to health throughout the lifespan and are increasingly recognized and studied for their roles in metabolic, immunological and neurological processes. Although the full complexity of these microbial communities is not fully understood, their clinical and industrial exploitation is well advanced and expanding, needing greater oversight guided by a consensus from the research community. One of the most controversial issues in microbiome research is the definition of a 'healthy' human microbiome. This concept is complicated by the microbial variability over different spatial and temporal scales along with the challenge of applying a unified definition to the spectrum of healthy microbiome configurations. In this Perspective, we examine the progress made and the key gaps that remain to be addressed to fully harness the benefits of the human microbiome. We propose a road map to expand our knowledge of the microbiome-health relationship, incorporating epidemiological approaches informed by the unique ecological characteristics of these communities.

The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directions

Antigen-specific B and T cell responses play a critical role in vaccine-mediated protection against infectious diseases, but these responses are highly variable between individuals and vaccine immunogenicity is frequently sub-optimal in infants, the elderly and in people living in low- and middle-income countries. Although many factors such as nutrition, age, sex, genetics, environmental exposures, and infections may all contribute to variable vaccine immunogenicity, mounting evidence indicates that the gut microbiota is an important and targetable factor shaping optimal immune responses to vaccination. In this review, we discuss evidence from human, preclinical and experimental studies supporting a role for a healthy gut microbiota in mediating optimal vaccine immunogenicity, including the immunogenicity of COVID-19 vaccines. Furthermore, we provide an overview of the potential mechanisms through which this could occur and discuss strategies that could be used to target the microbiota to boost vaccine immunogenicity where it is currently sub-optimal.

Pharmacological treatment for metabolic dysfunction-associated steatotic liver disease and related disorders: Current and emerging therapeutic options

Metabolic dysfunction-associated steatotic liver disease (MASLD; formerly known as nonalcoholic fatty liver disease) is a chronic liver disease affecting over a billion individuals worldwide. MASLD can gradually develop into more severe liver pathologies, including metabolic dysfunction-associated steatohepatitis (MASH), cirrhosis, and liver malignancy. Notably, although being a global health problem, there are very limited therapeutic options against MASLD and its related diseases. While a thyroid hormone receptor agonist (resmetirom) is recently approved for MASH treatment, other efforts to control these diseases remain unsatisfactory. Given the projected rise in MASLD and MASH incidence, it is urgent to develop novel and effective therapeutic strategies against these prevalent liver diseases. In this article, the pathogenic mechanisms of MASLD and MASH, including insulin resistance, dysregulated nuclear receptor signaling, and genetic risk factors (eg, patatin-like phospholipase domain-containing 3 and hydroxysteroid 17-β dehydrogenase-13), are introduced. Various therapeutic interventions against MASH are then explored, including approved medication (resmetirom), drugs that are currently in clinical trials (eg, glucagon-like peptide 1 receptor agonist, fibroblast growth factor 21 analog, and PPAR agonist), and those failed in previous trials (eg, obeticholic acid and stearoyl-CoA desaturase 1 antagonist). Moreover, given that the role of gut microbes in MASLD is increasingly acknowledged, alterations in the gut microbiota and microbial mechanisms in MASLD development are elucidated. Therapeutic approaches that target the gut microbiota (eg, dietary intervention and probiotics) against MASLD and related diseases are further explored. With better understanding of the multifaceted pathogenic mechanisms, the development of innovative therapeutics that target the root causes of MASLD and MASH is greatly facilitated. The possibility of alleviating MASH and achieving better patient outcomes is within reach. SIGNIFICANCE STATEMENT: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease worldwide, and it can progress to more severe pathologies, including steatohepatitis, cirrhosis, and liver cancer. Better understanding of the pathogenic mechanisms of these diseases has facilitated the development of innovative therapeutic strategies. Moreover, increasing evidence has illustrated the crucial role of gut microbiota in the pathogenesis of MASLD and related diseases. It may be clinically feasible to target gut microbes to alleviate MASLD in the future.

ImmunoMet Oncogenesis: A New Concept to Understand the Molecular Drivers of Cancer

The appearance of cancer progresses through a multistep process that includes genetic, epigenetic, mutational, inflammatory and metabolic disturbances to signaling pathways within an organ. The combined influence of these changes will dictate the growth properties of the cells; the direction of further malignancy depends on the severity of these "disturbances". The molecular mechanisms driving abnormal inflammation and metabolism are beginning to be identified and, in some cases, are quite prominent in pre-condition states of cancer and are significant drivers of the malignant phenotype. As such, utilizing signaling pathways linked to inflammation and metabolism as biomarkers of cancer is an emerging method and includes pathways beyond those well characterized to drive metabolism or inflammation. In this review, we will discuss several emerging elements influencing proliferation, inflammation and metabolism that may play a part as drivers of the cancer phenotype. These include AMPK and leptin (linked to metabolism), NOD2/RIPK2, TAK1 (linked to inflammation), lactate and pyruvate transporters (monocarboxylate transporter [MCT], linked to mitochondrial biogenesis and metabolism) and RASSF1A (linked to proliferation, cell death, cell cycle control, inflammation and epigenetics). We speculate that the aforementioned elements are important drivers of carcinogenesis that should be collectively referenced as being involved in "ImmunoMET Oncogenesis", a new tripartite description of the role of elements in driving cancer. This term would suggest that for a better understanding of cancer, we need to understand how proliferation, inflammation and metabolic pathways are impacted and how they influence classical drivers of malignant transformation in order to drive ImmunoMET oncogenesis and the malignant state.

Impact of Preoperative Biliary Stenting on Intestinal Dysfunction and Perioperative Complications After Pylorus-Preserving Pancreaticoduodenectomy

Background and Objectives: Preoperative biliary stenting (PBS) is commonly used to manage obstructive jaundice in patients undergoing pylorus-preserving pancreaticoduodenectomy (PPPD). However, the impact of PBS on intestinal barrier function and perioperative complications remains controversial. This study aims to evaluate the effect of PBS on intestinal dysfunction and surgical outcomes, focusing on the influence of the stent duration. Materials and Methods: In this prospective cohort study, 235 patients undergoing PPPD for resectable pancreatic neoplasms at Timișoara Municipal Emergency Clinical Hospital (2016-2024) were analyzed. Patients were divided into two groups: those with PBS (n = 98) and without PBS (n = 137). Intestinal barrier function was assessed pre- and postoperatively using biomarkers such as zonulin, fecal calprotectin, and serum lipopolysaccharides (LPS). Perioperative outcomes, including pancreatic fistula, delayed gastric emptying (DGE), infections, and hospital stay, were compared. Additionally, outcomes were stratified based on stent duration (2-3 weeks vs. 3-4 weeks). Results: PBS was associated with significantly higher levels of zonulin, fecal calprotectin, and serum LPS postoperatively, indicating compromised intestinal barrier function. The stented group had a higher incidence of pancreatic fistulas (Grade B/C: 27.5% vs. 13.1%, p < 0.01), DGE (25.5% vs. 13.1%, p = 0.008), postoperative infections (34.7% vs. 17.5%, p = 0.002), and prolonged hospital stay (16.9 ± 4.2 days vs. 14.5 ± 3.7 days, p = 0.019). Prolonged stenting (3-4 weeks) was associated with worse outcomes compared to shorter stenting durations (2-3 weeks), including increased rates of infections, sepsis, and ICU stay (p < 0.05 for all comparisons). Conclusions: Preoperative biliary stenting is associated with increased intestinal barrier dysfunction, systemic inflammation, and higher rates of perioperative complications following PPPD. Prolonged stenting durations (>3 weeks) further exacerbate these risks. Limiting the PBS duration to 2-3 weeks, alongside optimized perioperative management, may help reduce postoperative morbidity and improve surgical outcomes.

Coix Seed Extract Attenuates Glycolipid Metabolism Disorder in Hyperlipidemia Mice Through PPAR Signaling Pathway Based on Metabolomics and Network Pharmacology

Hyperlipidemia is characterized by a high level of blood lipid which poses a serious threat to human health. Coix seed is a traditional crop of medicine and food homology with a wide range of pharmacological actions. To make clear the attenuation effect of coix seed against hyperlipidemia, low and high doses of coix seed extract (CSE) were orally administered to hyperlipidemia model mice developed by high-fat diet (HFD). Our results showed that CSE notably improved liver pathological injury, and oxidative stress, and declined the levels of glucose and lipid in hyperlipidemia mice. Liver metabolomics showed that lipid-related metabolites notably decreased, and pathways of glycolipid metabolism were seriously affected by CSE intervention. Moreover, 16S rRNA sequencing revealed that CSE treatment notably increased the diversity of gut microbiota. Meanwhile, the microbiota with the function of regulating intestinal balance as well as relieving obesity and nervous diseases significantly enhanced while harmful flora notably decreased after CSE intervention. The results of network pharmacology and molecular docking indicated that the PPAR signaling pathway may be the core path of anti-hyperlipidemia for coix seeds. RT-qPCR further verified that the expression levels of genes from the PPAR pathway notably changed by CSE treatment with fat synthesis genes significantly decreased while lipolysis genes notably enhanced. Therefore, coix seed might be a potential candidate for the treatment of hyperlipidemia.

A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites

Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.

Conjunctival microbiota variations in a subset of middle-aged and elderly individuals from Beijing, China

AIM

To isolate and identify the conjunctival microbiota of cataract patients and analyze the associated influencing factors.

METHODS

This study recruited 216 participants (216 eyes) from April 2022 to July 2022. Under the condition of no antibiotic use prior to cataract surgery, sterile swabs were used to collect samples from the lower conjunctival sac. Bacterial cultures were then conducted, followed by species identification through 16S rDNA gene sequencing. Clinical factors associated with positive or negative bacterial isolation rates were analyzed, including age, gender, meibomian gland dysfunction (MGD), history of hypertension, history of diabetes, history of cancer, history of infectious diseases and the habit of wearing masks.

RESULTS

Among the 216 eyes, 78 eyes yielded isolates, with an isolation rate of 36.11%, detecting a total of 122 strains. Gram-positive rods accounted for 49.18% (60 strains), gram-positive cocci accounted for 45.08% (55 strains), gram-negative bacteria accounted for 4.92% (6 strains), and fungi accounted for 0.82% (1 strain). This study found that the most abundant genera in the conjunctival sac were Corynebacterium (42.62%), Staphylococcus (31.15%), Micrococcus (9.84%), Acinetobacter (4.10%), and Bacillus (3.28%). Furthermore, age (P=0.006), gender (P=0.039), diabetes (P=0.003), history of infectious diseases (P=0.02), and duration of mask replacement (P<0.001) were important factors influencing the positive bacterial culture of the conjunctival microbiota. Although hypertensive patients exhibited a higher isolation rate of conjunctival bacteria, it did not reach statistical significance, and the history of cancer did not affect the isolation rate of the conjunctival microbial community in cataract patients before surgery.

CONCLUSION

Potential changes are observed in the conjunctival microbiota among a sample of middle-aged and elderly individuals from Beijing, China. Notably, an increased isolation rate of Corynebacterium and Micrococcus is detected, suggesting a possible change in the microbial balance that requires further investigation and attention from the ophthalmological community. Advanced age, female gender, MGD, diabetes, a recent history of infectious diseases, and inadequate mask-wearing habits are potentially significant factors associated with the conjunctival microbiota. These factors should be considered in the development of strategies to prevent perioperative infections in cataract surgery patients.

The Potential Role of Microbiota in Age-Related Cognitive Decline: A Narrative Review of the Underlying Molecular Mechanisms

As the world's population continues to age, social patterns are changing, making aging a notable public health challenge. With aging as the major risk factor for cognitive decline, the global prevalence of dementia is projected to triple in the next 25 years. In light of the growing body of evidence of the involvement of microbiota in health and pathology, its role in age-related cognitive decline should be explored. Therefore, the aim of this narrative review is to thoroughly analyze the ways in which microbiota might affect the aging process and age-related cognitive decline. Overall, aging is a complex phenomenon manifested at systemic, cellular and molecular levels. According to recent studies, gut microbiota composition may influence age-related changes through the gut-brain axis. One mechanism involves dysbiosis-related chronic systemic inflammation, leading to the blood-brain barrier disruption and subsequent neuroinflammatory processes. In addition to inflammaging, gut microbiota may induce oxidative stress, which is another key factor in brain aging. Finally, not only gut microbiota, but also microbiota colonizing the oral cavity may be associated with age-related neurodegenerative diseases.

PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis

BACKGROUND

Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.

RESULTS

Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/ ), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.

CONCLUSIONS

Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.

Atopic Dermatitis and Atopic Keratoconjunctivitis: New Insights in the Analyses of Microbiota and Probiotic Effect

Atopy is defined as a predisposition to hypersensitivity reactions against a range of antigens. It is characterized by the activation of CD4+ T helper type 2 (Th2) cells and an increased production of immunoglobulin E (IgE). The most common atopic conditions are atopic dermatitis, asthma, allergic rhinitis, food allergies, and atopic ocular diseases. Atopic keratoconjunctivitis (AKC) is a chronic, bilateral inflammatory condition affecting the ocular surface, frequently occurring in conjunction with atopic dermatitis. It is not uncommon for patients to present with multiple conditions simultaneously or in a sequential manner. A comprehensive understanding of the underlying mechanisms of atopic diseases is essential for the effective clinical evaluation and treatment. Recent research has underscored the pivotal role of the microbiota in the pathogenesis of atopic dermatitis and atopic eye diseases, with alterations in microbial composition (dysbiosis) being linked to a spectrum of atopic conditions. Probiotics are currently being investigated as a potential treatment option for restoring microbial balance and alleviating disease symptoms. This review examines the relationship between atopic dermatitis, atopic keratoconjunctivitis, and the microbiota, evaluating the current evidence and exploring the potential of probiotics as a novel therapeutic approach.

On-orbit microbial succession patterns of the China Space Station during the construction period

BACKGROUND

The China Space Station (CSS) modules feature many areas that are difficult to clean and thus susceptible to microbial outbreaks. A new sampling method utilizing an equivalent material sheet was applied to characterize the diversity of microbes that accumulated in inaccessible areas in orbit on the CSS. Equivalent material sheet is a membrane made of the same material as the wall of the module.

RESULTS

Fifty samples were collected from interior surfaces (work, sleeping, and sanitary areas) of the Tianhe core module and the Wentian and Mengtian experimental modules, covering three flights by the Shenzhou (SZ)-12 to SZ-14 astronaut crews from 2021 to 2022. The numbers of culturable bacteria and fungi that accumulated during the on-orbit periods of each flight ranged from 0 to 2.83 × 109 colony-forming units/100 cm2. The number of bacteria detected by quantitative PCR (qPCR) ranged from 1.24 × 105 to 2.59 × 109 rRNA gene copies/100 cm2, with an average viability of 65.08%. A total of 103 bacterial strains and 27 fungal strains were cultured and isolated. The dominant culturable microorganisms were mainly from the genera Bacillus, Staphylococcus, Aspergillus, Cladosporium, and Penicillium. High-throughput sequencing results showed that the predominant bacteria were Pseudomonas, Stenotrophomonas, Methylobacterium-Methylorubrum, Sphingomonas, Bacillus, Staphylococcus, and Nocardiopsis. The microbial diversity in each module varied significantly with sampling time and sampling area. In the early stage of CSS construction with the SZ-12 crew, the microbial species evenness in the modules was high; later, with the SZ-13 crew, Pseudomonas began to appear as the dominant microorganism. More than half (58.80%) of the bacteria on module surfaces originated from the human skin and oral environments. Lactobacillus was present in all areas of the three modules at all sampling times. The biomarker bacteria Stenotrophomonas sp., isolated from the work area in the Tianhe core module, are typically derived from plants. SourceTracker analysis indicated that most of the microbes in the orbiting CSS came from human bodies, and that microbial diversity was significantly altered with each crew change.

CONCLUSION

Future efforts at microbial prevention and control on orbit should emphasize the human and plant origins of microbes. Information on the microbial diversity in the condensate zone could be useful to guide the development of new strategies to prevent and control microbes during space flight. Video Abstract.

Exploring the Multifaceted Therapeutic Potential of Probiotics: A Review of Current Insights and Applications

The interplay between human health and the microbiome has gained extensive attention, with probiotics emerging as pivotal therapeutic agents due to their vast potential in treating various health issues. As significant modulators of the gut microbiota, probiotics are crucial in maintaining intestinal homeostasis and enhancing the synthesis of short-chain fatty acids. Despite extensive research over the past decades, there remains an urgent need for a comprehensive and detailed review that encapsulates probiotics' latest insights and applications. This review focusses on the multifaceted roles of probiotics in promoting health and preventing disease, highlighting the complex mechanisms through which these beneficial bacteria influence both gut flora and the human body at large. This paper also explores probiotics' neurological and gastrointestinal applications, focussing on their significant impact on the gut-brain axis and their therapeutic potential in a broad spectrum of pathological conditions. Current innovations in probiotic formulations, mainly focusing on integrating genomics and biotechnological advancements, have also been comprehensively discussed herein. This paper also critically examines the regulatory landscape that governs probiotic use, ensuring safety and efficacy in clinical and dietary settings. By presenting a comprehensive overview of recent studies and emerging trends, this review aims to illuminate probiotics' extensive therapeutic capabilities, leading to future research and clinical applications. However, besides extensive research, further advanced explorations into probiotic interactions and mechanisms will be essential for developing more targeted and effective therapeutic strategies, potentially revolutionizing health care practices for consumers.

Bacterial small molecule metabolites implicated in gastrointestinal cancer development

Numerous associations have been identified between cancer and the composition and function of the human microbiome. As cancer remains the second leading global cause of mortality, investigating the carcinogenic contributions of microbiome members could advance our understanding of cancer risk and support potential therapeutic interventions. Although fluctuations in bacterial species have been associated with cancer progression, studying their small molecule metabolites offers one avenue to establish support for causal relationships and the molecular mechanisms governing host-microorganism interactions. In this Review, we explore the expanding repertoire of small molecule metabolites and their mechanisms implicated in the risk of developing gastrointestinal cancers.

A review on gut microbiota and miRNA crosstalk: implications for Alzheimer's disease

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and progressive neuronal damage. Recent research has highlighted the significant roles of the gut microbiota and microRNAs (miRNAs) in the pathogenesis of AD. This review explores the intricate interaction between gut microbiota and miRNAs, emphasizing their combined impact on Alzheimer's progression. First, we discuss the bidirectional communication within the gut-brain axis and how gut dysbiosis contributes to neuroinflammation and neurodegeneration in AD. Changes in gut microbiota composition in Alzheimer's patients have been linked to inflammation, which exacerbates disease progression. Next, we delve into the biology of miRNAs, focusing on their roles in gene regulation, neurodevelopment, and neurodegeneration. Dysregulated miRNAs are implicated in AD pathogenesis, influencing key processes like inflammation, tau pathology, and amyloid deposition. We then examine how the gut microbiota modulates miRNA expression, particularly in the brain, potentially altering neuroinflammatory responses and synaptic plasticity. The interplay between gut microbiota and miRNAs also affects blood-brain barrier integrity, further contributing to Alzheimer's pathology. Lastly, we explore therapeutic strategies targeting this gut microbiota-miRNA axis, including probiotics, prebiotics, and dietary interventions, aiming to modulate miRNA expression and improve AD outcomes. While promising, challenges remain in fully elucidating these interactions and translating them into effective therapies. This review highlights the importance of understanding the gut microbiota-miRNA relationship in AD, offering potential pathways for novel therapeutic approaches aimed at mitigating the disease's progression.

Gut Microbiota-Tumor Microenvironment Interactions: Mechanisms and Clinical Implications for Immune Checkpoint Inhibitor Efficacy in Cancer

Cancer immunotherapy has transformed cancer treatment in recent years, with immune checkpoint inhibitors (ICIs) emerging as a key therapeutic approach. ICIs work by inhibiting the mechanisms that allow tumors to evade immune detection. Although ICIs have shown promising results, especially in solid tumors, patient responses vary widely due to multiple intrinsic and extrinsic factors within the tumor microenvironment. Emerging evidence suggests that the gut microbiota plays a pivotal role in modulating immune responses at the tumor site and may even influence treatment outcomes in cancer patients receiving ICIs. This review explores the complex interactions between the gut microbiota and the tumor microenvironment, examining how these interactions could impact the effectiveness of ICI therapy. Furthermore, we discuss how dysbiosis, an imbalance in gut microbiota composition, may contribute to resistance to ICIs, and highlight microbiota-targeted strategies to potentially overcome this challenge. Additionally, we review recent studies investigating the diagnostic potential of microbiota profiles in cancer patients, considering how microbial markers might aid in early detection and stratification of patient responses to ICIs. By integrating insights from recent preclinical and clinical studies, we aim to shed light on the potential of microbiome modulation as an adjunct to cancer immunotherapy and as a diagnostic tool, paving the way for personalized therapeutic approaches that optimize patient outcomes.

Metagenome-guided culturomics for the targeted enrichment of gut microbes

The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.

Associations among rearing environment and the infant gut microbiome with early-life neurodevelopment and cognitive development in a nonhuman primate model (Macaca mulatta)

Early gut microbiome development may impact brain and behavioral development. Using a nonhuman primate model (Macaca mulatta), we investigated the association between social environments and the gut microbiome on infant neurodevelopment and cognitive function. Infant rhesus monkeys (n = 33) were either mother-peer-reared (MPR) or nursery-reared (NR). Neurodevelopmental outcomes, namely emotional responsivity, visual orientation, and motor maturity, were assessed with the Primate Neonatal Neurobehavioral Assessment (PNNA) at 14-30 days. Cognitive development was assessed through tasks evaluating infant reward association, cognitive flexibility, and impulsivity at 6-8 months. The fecal microbiome was quantified from rectal swabs via 16S rRNA sequencing. Factor analysis was used to identify "co-abundance factors" describing patterns of microbial composition. We used multiple linear regressions with AIC Model Selection and differential abundance analysis (MaAsLin2) to evaluate relationships between co-abundance factors, microbiome diversity, and neuro-/cognitive development outcomes. At 30 days of age, a gut microbiome co-abundance factor, or pattern, with high Prevotella and Lactobacillus (β = -0.88, p = 0.04, AIC Weight = 68%) and gut microbiome alpha diversity as measured by Shannon diversity (β = -1.33, p = 0.02, AIC Weight = 80%) were both negatively associated with infant emotional responsivity. At 30 days of age, being NR was also associated with lower emotional responsivity (Factor 1 model: β = -3.13, p < 0.01; Shannon diversity model: β = -3.77, p < 0.01). The infant gut microbiome, along with early-rearing environments, may shape domains of neuro-/cognitive development related to temperament.

Impact of Early-Life Microbiota on Immune System Development and Allergic Disorders

Introduction: The shaping of the human intestinal microbiota starts during the intrauterine period and continues through the subsequent stages of extrauterine life. The microbiota plays a significant role in the predisposition and development of immune diseases, as well as various inflammatory processes. Importantly, the proper colonization of the fetal digestive system is influenced by maternal microbiota, the method of pregnancy completion and the further formation of the microbiota. In the subsequent stages of a child's life, breastfeeding, diet and the use of antibiotics influence the state of eubiosis, which determines proper growth and development from the neonatal period to adulthood. The literature data suggest that there is evidence to confirm that the intestinal microbiota of the infant plays an important role in regulating the immune response associated with the development of allergic diseases. However, the identification of specific bacterial species in relation to specific types of reactions in allergic diseases is the basic problem. Background: The main aim of the review was to demonstrate the influence of the microbiota of the mother, fetus and newborn on the functioning of the immune system in the context of allergies and asthma. Methods: We reviewed and thoroughly analyzed the content of over 1000 articles and abstracts between the beginning of June and the end of August 2024. Over 150 articles were selected for the detailed study. Results: The selection was based on the PubMed National Library of Medicine search engine, using selected keywords: "the impact of intestinal microbiota on the development of immune diseases and asthma", "intestinal microbiota and allergic diseases", "the impact of intrauterine microbiota on the development of asthma", "intrauterine microbiota and immune diseases", "intrauterine microbiota and atopic dermatitis", "intrauterine microbiota and food allergies", "maternal microbiota", "fetal microbiota" and "neonatal microbiota". The above relationships constituted the main criteria for including articles in the analysis. Conclusions: In the present review, we showed a relationship between the proper maternal microbiota and the normal functioning of the fetal and neonatal immune system. The state of eubiosis with an adequate amount and diversity of microbiota is essential in preventing the development of immune and allergic diseases. The way the microbiota is shaped, resulting from the health-promoting behavior of pregnant women, the rational conduct of the medical staff and the proper performance of the diagnostic and therapeutic process, is necessary to maintain the health of the mother and the child. Therefore, an appropriate lifestyle, rational antibiotic therapy as well as the way of completing the pregnancy are indispensable in the prevention of the above conditions. At the same time, considering the intestinal microbiota of the newborn in relation to the genera and phyla of bacteria that have a potentially protective effect, it is worth noting that the use of suitable probiotics and prebiotics seems to contribute to the protective effect.

Distinct Ocular Surface Microbiome in Keratoconus Patients Correlate With Local Immune Dysregulation

Purpose

Keratoconus (KC) is characterized by irregular astigmatism along with corneal stromal weakness and is associated with altered immune status. Tissue resident microbiomes are known to influence the immune status in other organs, but such a nexus has not been described in ocular conditions. Therefore, we examined the ocular surface microbiome of patients with KC and correlated it to the immune cell and tear molecular factor profiles.

Methods

Sixty-two patients with KC and 21 healthy controls underwent corneal topography analysis and eye examination followed by a collection of Schirmer's strip, ocular surface wash, and ocular surface swabs. Microbiomes were analyzed by extracting DNA from the swabs followed by 16S rRNA gene V3-V4 amplicon sequencing and analyzed using QIIME. Fifty-two molecular factors from Schirmer's strip tear extracts and 11 immune cells from ocular wash were measured using multiplex ELISA and flow cytometry. Alpha diversity, linear discriminant analysis effect size (LEfSe), relative abundance and receiver operating characteristic - area under the curve (ROC-AUC) analysis were performed. Unsupervised clustering at the genus level with clinical parameters, soluble factors, and immune cells was performed.

Results

Fifty-two phyla/class, 132 order, 283 family, and 718 genera were identified in our cohort. Alpha diversity indices were comparable between patients with KC and the healthy controls. Dominant phyla across groups were Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Alphaproteobacteria increased in KC eyes whereas Actinobacteria, Firmicutes_Bacilli reduced compared with the healthy controls. We found a significant positive correlation of Microbacterium, Cutibacterium, and Brevundimonas genera abundance with keratometry and corneal thickness. Levels of IL-21, IL-9, Fractalkine, and VEGF positively correlated with Tetrasphaera (P < 0.05). β2-microglobulin and CD66bhigh cells correlated with Bacteroides (P < 0.05). CD45+ cells correlated with Escherichia_Shigella (P < 0.02).

Conclusions

We discovered a unique microbiome signature of KC which correlated to disease grades and secreted molecular factors and immune cells. Therefore, the altered microbiome on the ocular surface may drive immune dysregulation in KC and provide scope for potential interventions in the future.

Mechanistic insight of neurodegeneration due to micro/nano-plastic-induced gut dysbiosis

Despite offering significant conveniences, plastic materials contribute substantially in developing environmental hazards and pollutants. Plastic trash that has not been adequately managed may eventually break down into fragments caused by human or ecological factors. Arguably, the crucial element for determining the biological toxicities of plastics are micro/nano-forms of plastics (MPs/NPs), which infiltrate the mammalian tissue through different media and routes. Infiltration of MPs/NPs across the intestinal barrier leads to microbial architectural dysfunction, which further modulates the population of gastrointestinal microbes. Thereby, it triggers inflammatory mediators (e.g., IL-1α/β, TNF-α, and IFN-γ) by activating specific receptors located in the gut barrier. Mounting evidence indicates that MPs/NPs disrupt host pathophysiological function through modification of junctional proteins and effector cells. Moreover, the alteration of microbial diversity by MPs/NPs causes the breakdown of the blood-brain barrier and translocation of metabolites (e.g., SCFAs, LPS) through the vagus nerve. Potent penetration affects the neuronal networks, neuronal protein accumulation, acceleration of oxidative stress, and alteration of neurofibrillary tangles, and hinders distinctive communicating pathways. Conclusively, alterations of these neurotoxic factors are possibly responsible for the associated neurodegenerative disorders due to the exposure of MPs/NPs. In this review, the hypothesis on MPs/NPs associated with gut microbial dysbiosis has been interlinked to the distinct neurological impairment through the gut-brain axis.

Covariation Between Microbiome Composition and Host Transcriptome in the Gut of Wild Drosophila melanogaster: A Re-Analysis

Gut microbiota are fundamental for healthy animal function, but the evidence that host function can be predicted from microbiota taxonomy remains equivocal, and natural populations remain understudied compared to laboratory animals. Paired analyses of covariation in microbiota and host parameters are powerful approaches to characterise host-microbiome relationships mechanistically, especially in wild populations of animals that are also lab models, enabling insight into the ecological basis of host function at molecular and cellular levels. The fruitfly Drosophila melanogaster is a preeminent model organism, amenable to field investigation by 'omic analyses. Previous work in wild male D. melanogaster guts analysed paired measurements of (A) bacterial diversity and abundance, measured by 16S amplicon sequencing; and (B) the host gut transcriptome, but no signature of covariation was detected. Here, we re-analyse those data comprehensively. We find orthogonal axes of microbial genera, which correspond to differential expression of host genes. The differentially expressed gene sets were enriched in functions including protein translation, mitochondrial respiration, immunity and reproduction. Each gene set had a distinct functional signature, suggesting that wild flies exhibit a range of distinct axes of functional variation, which correspond to orthogonal axes of microbiome variation. These findings lay a foundation to better connect ecology and functional genetics of a leading host-microbiome model.

Ameliorative effects of insoluble dietary fiber and its bound polyphenols from adzuki bean seed coat on acute murine colitis induced by DSS: The inflammatory response, intestinal barrier and gut microbiota

The incidence of ulcerative colitis (UC) is closely associated with dietary fiber (DF) intake. This study aims to evaluate the ameliorative effects of insoluble dietary fiber from adzuki bean seed coat (AIDF) on dextran sulfate sodium (DSS)-induced UC in mice, both with and without bound polyphenols (BPs). We employed a model based on the "remove/backfill" of components. Compared to dephenolized dietary fiber (AIDF-DF) and AIDF-DF with replaced BPs (AIDF-BP), AIDF was found to effectively reduce the splenic index, alleviate colonic histopathological damage, lower serum levels of inflammatory mediators (TNF-α, IL-1β, IFN-γ, IL-6), decrease activities of LPS, DAO, MPO, and iNOS, regulate intestinal tight junction (TJ) mRNA and protein expression, and restore the integrity of the colonic epithelial cell barrier. AIDF mitigated the inflammatory response in UC by inhibiting the TLR4/NF-κB inflammatory signaling pathway. It increased the abundance of beneficial gut microbiota (e.g., Akkermansia, Verrucomicrobiota) while reducing the abundance of harmful bacteria (e.g., Proteobacteria), thereby alleviating intestinal disturbances in DSS-induced colitis in mice. In conclusion, the presence of BPs in AIDF plays a critical role in attenuating DSS-induced UC in mice.

Tissue source may affect the esophageal flora in patients with esophageal squamous cell carcinoma

The aim of the present study was to provide a theoretical basis for the selection of standard sampling methods in the study of the esophageal microbiota in patients with esophageal squamous cell carcinoma (ESCC) by comparing the differences in bacterial communities between surgical and endoscopic esophageal mucosal tissues. A total of 72 patients with ESCC who were diagnosed at Taihe Hospital (Shiyan, China) between July 2018 and July 2019 were selected to participate in the present study. The sequence V4 hypervariable region was amplified, and Illumina HiSeq sequencing was performed to analyze the differences between the two groups. The Shannon and Chao1 indices of the postoperative esophageal cancer tissue group samples (Group A) were higher than those of the esophageal mucosa tissue samples (Group B), and the difference was statistically significant (P<0.05). The Simpson index of Group A was higher than that of Group B, but the difference was not significant (P>0.05). The β diversity analysis demonstrated that the overall composition of the flora of the two groups was not significantly different. Linear discriminant analysis effect size analysis showed that the abundance of Megasphaera, Actinobacteria, Enterobacteriaceae and Enterobacteriales in Group A was significantly higher than that in Group B, but the abundance of Mogibacteriaceae in Group B was significantly higher than that in Group A. The top 60 species were selected using the random forest method to establish a model. The error rate of the prediction model constructed using the random forest method was 22.59%. The receiver operating characteristic (ROC) curve analysis confirmed that the present model was reliable and could effectively distinguish between the two groups of samples (area under the curve, 0.86). The source of the sample should be considered in studies investigating the esophageal flora. Considering the increased richness and improved uniformity of postoperative tissue microbiota compared with the mucosal group, it was predicted that postoperative tissue may be more conducive to the study of esophageal cancer microbiota.

Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units

The microbiome is increasingly regarded as a key component of human health, and analysis of microbiome data can aid in the development of precision medicine. Due to the high cost of shotgun metagenomic sequencing (SM-seq), microbiome analyses can be done cost-effectively in two phases: Phase 1-sequencing of 16S ribosomal RNA, and Phase 2-SM-seq of an informative subsample. Existing research suggests strategies to select the subsample based on biological diversity and dissimilarity metrics calculated using operational taxonomic units (OTUs). However, the microbiome field has progressed towards amplicon sequencing variants (ASVs), as they provide more precise microbe identification and sample diversity information. The aim of this work is to compare the subsampling strategies for two-phase metagenomic studies when using ASVs instead of OTUs, and to propose data driven strategies for subsample selection through dimension reduction techniques. We used 199 samples of infant-gut microbiome data from the DIABIMMUNE project to generate ASVs and OTUs, then generated subsamples based on five existing biologically driven subsampling methods and two data driven methods. Linear discriminant analysis Effect Size (LEfSe) was used to assess differential representation of taxa between the subsamples and the overall sample. The use of ASVs showed a 50-93% agreement in the subsample selection with the use of OTUs for the subsampling methods evaluated, and showed a similar bacterial representation across all methods. Although sampling using ASVs and OTUs typically lead to similar results for each subsample, ASVs had more clades that differed in expression levels between allergic and non-allergic individuals across all sample sizes compared to OTUs, and led to more biomarkers discovered at Phase 2-SM-seq level.

Effects of probiotics in elderly hospitalized tube-fed patients with antibiotics use

BACKGROUND

Several studies revealed the beneficial effects of probiotics against the incidence of antibiotic-associated diarrhea of hospitalized patients but it is rarely to assess the nutrition status. This study investigated the effects of probiotics in elderly hospitalized tube-fed patients with antibiotics use and is the first study that concerns the nutritional status among these patients.

METHODS

Elderly hospitalized tube-fed patients who were using antibiotics were recruited. Probiotics were given within 48 h after their first antibiotic therapy, and then twice daily 2 h after consuming antibiotics and a meal; the probiotics were continued to use for an additional 7 days after completion of antibiotics therapy. Anthropometric data, laboratory data, medication records, nutritional status, nutrition intake and data on stool form were collected.

RESULTS

Twenty-nine patients served as probiotic group. 11 patients completed the study in both groups. In probiotic group, the stool form was found to exhibit no significant differences between the beginning and end of antibiotics therapy (5.5 ± 0.8 vs 5.1 ± 1.1, p = 0.21), but the stool frequency significantly decreased (2.0 ± 1.0 vs 1.6 ± 0.7, p = 0.05). In control group, the stool form between the beginning and end of antibiotics therapy exhibited significant improvement (5.6 ± 1.4 vs 4.5 ± 1.4, p = 0.01), but not in the frequency (2.7 ± 2.1 vs 2.4 ± 1.5, p = 0.1). The initial NRS 2002 score of the probiotic and control groups were similar. (3.6 ± 1.7 vs 3.7 ± 1.8, p = 1.00), and their nutrition status both significantly improved during the last visit before discharged (2.6 ± 0.9 vs 2.9 ± 1.3).

CONCLUSION

Probiotic supplementation in elderly hospitalized tube-fed patients significantly reduced stool frequency during antibiotic treatment. Improvements in stool form were observed only during the follow-up period. Nutritional status remained stable, with patients' nutritional needs adequately met throughout the study.

RFW captures species-level metagenomic functions by integrating genome annotation information

Functional profiling of whole-metagenome shotgun sequencing (WMS) enables our understanding of microbe-host interactions. We demonstrate microbial functional information loss by current annotation methods at both the taxon and community levels, particularly at lower read depths. To address information loss, we develop a framework, RFW (reference-based functional profile inference on WMS), that utilizes information from genome functional annotations and taxonomic profiles to infer microbial function abundances from WMS. Furthermore, we provide an algorithm for absolute abundance change quantification between groups as part of the RFW framework. By applying RFW to several datasets related to autism spectrum disorder and colorectal cancer, we show that RFW augments downstream analyses, such as differential microbial function identification and association analysis between microbial function and host phenotype. RFW is open source and freely available at https://github.com/Xingyinliu-Lab/RFW.