The Human Gut Microbiome: From Association to Modulation

Effectiveness of newly isolated bacteriophages targeting multidrug-resistant Extraintestinal Pathogenic Escherichia coli strain (TZ1_3) in food preservation and mice health modulation

Bacteriophages are promising alternatives for combating multidrug-resistant bacterial infections. Two lytic bacteriophages, named P1 and P3, targeting pathogenic Escherichia coli (ExPEC; strain TZ1_3) were isolated and evaluated for their potential ability to control pathogenic numbers either in ExPEC-contaminated food or ExPEC-infected mice. Results showed that phages significantly reduced ExPEC numbers within 6 and 12 h in contaminated water, milk, beef, and chicken when applied at 106 plaque-forming units (PFU). Notably, phage therapy administered via intraperitoneal injection (1012 PFU) effectively reduced ExPEC numbers in the heart, liver, spleen and kidney, restored α-diversity of gut microbes, and increased levels of acetic (13.98 %-37.58 %) and valeric acid (10.27 %-31.51 %) in ExPEC-infected mice. Additionally, phage injections caused no detrimental effects on body weight (which increased by 6.49 %-8.11 %), and on gut microbes in healthy mice. Overall, this study highlights the potential of phages in controlling foodborne microorganisms.

Biological activities, biosynthetic capacity and metabolic interactions of lactic acid bacteria and yeast strains from traditional home-made kefir

Given the widespread industrial and domestic use of probiotic blends based on combinations of lactic acid bacteria (LAB) and yeasts to produce fermented foods or beverages that are supposed to provide health benefits, this study aimed to generate knowledge and concepts on biologically relevant activities, metabolism and metabolic interactions in yeast/LAB communities. For this, the postbiotic capabilities of three probiotic candidates, including two lactic acid bacteria (i.e., Lactococcus lactis subsp. hordniae and Lactococcus lactis subsp. lactis) and the yeast Pichia kudriavzevii, isolated from a traditional home-made kefir, were explored combining an assortment of bioassays with a GC-MS footprint metabolomic strategy. Cell-free supernatants from cultures showed antimicrobial/antioxidant activity and inhibited biofilm formation by Salmonella sp. Several bioactive secondary metabolites (including tyrosol, phenylethyl alcohol, 2,3-butanediol, erythritol, tryptophol, putrescine, cadaverine, 3-phenyllactate, 2-hydroxyisocaproate) were detected which may contribute to the odor and flavour of the fermented products and their effects on human body.

Specnuezhenide: Comprehensive review of pharmacology, pharmacokinetics and ethnomedicinal uses

BACKGROUND

Specnuezhenide (SPN) is a bioactive iridoid terpenoid compound mainly found in Ligustri Lucidi Fructus (LLF), that has a broad spectrum of pharmacological effects, including anti-neoplastic, hepatoprotective, anti-aging, anti-inflammatory, immune-modulatory properties.

PURPOSE

The present review provides a comprehensive summary of natural medicinal plants, traditional Chinese medicine compounds containing SPN, and their corresponding pharmacological mechanisms.

METHODS

Using several globally recognized databases such as Web of Science, Google Scholar, PubMed, ScienceDirect, Wiley, ACS, Springer, and CNKI until December 2024, A comprehensive literature search and analysis was carried out with the keywords "Specnuezhenide", " Pharmacology ", "Pharmacokinetics" and " Chinese herbal compound".

RESULTS

The results indicated that SPN is present in a diverse range of plants, including LLF, Osmanthus fragrans seeds and Naked barley. SPN plays an anti-inflammatory role by regulating the NF-κB and MAPK signaling pathways, down-regulating the expression of TNF-α, IL-1β, IL-6 and other cytokines. Furthermore, many Chinese herbal compounds have been found to contain SPN, such as treatment of spleen and kidney deficiency of compound Shenhua tablet, treatment of liver-kidney Yin deficiency of Er Zhi Wan, treatment of pulmonray abscess of Qidongning and treatment of stagnation of QI due to depression of the liver of Shuganzhi Tablet. SPN is primarily distributed in the stomach, intestine, and liver. However, due to its limited absorption in the gastrointestinal tract and low blood concentration, its bioavailability is significantly reduced.

CONCLUSIONS

Thereby, SPN holds immense potential in the prevention and treatment of liver, lung and kidney complications. This review intends to provide a novel insight for further development of SPN, hoping to reveal the potential of SPN and necessity of further studies in this field.

The gut microbiota in spondyloarthritis: an update

PURPOSE OF REVIEW

This review provides an updated overview of the gut microbiota's involvement in spondyloarthritis (SpA) from a clinical perspective. It explores mechanisms by which the gut microbiota may influence SpA pathogenesis and considers the therapeutic implications of targeting the microbiome in SpA treatment.

RECENT FINDINGS

The pathogenesis of SpA is multifactorial, involving genetic predisposition, external factors and dysregulation of the immune system. Recent studies have identified alterations in the gut microbiome of patients with SpA, including changes in microbial diversity and specific taxa linked to disease activity. HLA-B27 status seems to influence gut microbiota composition, potentially impacting disease progression. In HLA-B27 transgenic rats, the association between gut microbiota and SpA development has been confirmed, supporting findings from human studies. A compromised gut barrier, influenced by proteins like zonulin, may allow microbial antigens to translocate, triggering immune responses associated with SpA.

SUMMARY

These findings highlight the potential for microbiota-modulating therapies, such as probiotics, prebiotics, diet and exercise, in managing SpA. However, methodological variability in human studies exposes the need for more rigorous research to better understand these associations. This may offer the opportunity to refine treatment strategies, offering a personalized approach to managing the disease.

Systemic inflammation is associated with gut microbiota diversity in post-stroke patients

BACKGROUND

There is growing interest in gut microbiota and health outcomes. However, the relationship between systemic inflammation and gut microbiota diversity in hospitalized patients remains unclear. This study aimed to investigate the association in post-stroke rehabilitation patients.

METHODS

A cross-sectional study was conducted on post-stroke patients admitted to a rehabilitation hospital. Systemic inflammation was assessed using the modified Glasgow Prognostic Score (mGPS). Gut microbiota diversity was evaluated using three indices: Shannon index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analyses were performed to examine the relationship between mGPS and gut microbiota diversity indices, adjusting for potential confounders.

RESULTS

A total of 156 patients (mean age 78.4 years; 55.7% men) were analyzed. The median mGPS was 0 (interquartile range: 0-1), with GPS distribution: 61.8% scored 0, 25.7% scored 1, and 12.5% scored 2. After adjusting for confounders, mGPS was significantly and negatively associated with the Shannon index (B = -0.143, 95% CI -0.288 to -0.002, β = -0.177) and OTU richness (B = -17.832, 95% CI -24.349 to -3.951, β = -0.208). However, no significant association was observed between mGPS and Faith's PD (B = -1.155, 95% CI -2.464 to 0.189, β = -0.155).

CONCLUSION

This study demonstrates a significant negative association between systemic inflammation and both quantitative and qualitative gut microbiota diversity in post-stroke patients.

Impact of host physiology and external stressors on the bacterial community of Schmidtea mediterranea

To fully comprehend host-microorganism interactions, it is crucial to understand the composition and diversity of the microbiome, as well as the factors that shape these characteristics. We investigated microbiome variation using the freshwater planarian Schmidtea mediterranea, an invertebrate model in regeneration biology and (eco-)toxicology, by exposing the organisms to various controlled conditions. The microbiome composition exhibited high variability, with most of the bacteria belonging to the Betaproteobacteria. Among the diverse microbial communities, a few genera, such as Curvibacter, were consistently present, but exhibited significant alterations in response to changing conditions. The relative abundance of Curvibacter fluctuated during the regeneration process, initially increasing before returning to a composition similar to the beginning situation. After applying external stress, the relative abundance of Curvibacter and other genera decreased. Variation over time, between different origin laboratories and between individuals, showed that additional, yet to-be-identified, factors of variation are present. Taking all results together, our study provides a solid basis for future research focusing on bacterial functionality in planarians and other invertebrates.

Structural analysis of gum arabic side chains from Acacia seyal released by bifidobacterial β-arabino-oligosaccharide 3-O-β-l-arabinopyranosyl-α-l-arabinofuranosidase

Gum arabic is widely used in the food and beverage industries for its emulsifying, stabilizing, and prebiotic effects, which promote Bifidobacterium growth. The two commercially approved varieties of gum arabic, namely, Acacia senegal gum and A. seyal gum, predominantly consist of arabinogalactan protein (AGP), albeit with different side chain modifications. We previously characterized two enzymes belonging to glycoside hydrolase (GH) family 39 in bifidobacteria involved in the release of α-d-Gal-(1→3)-α-l-Ara and β-l-Arap-(1→3)-α-l-Ara from the side chains of A. senegal gum. Although the carbohydrate structure of A. senegal gum is being increasingly explored, limited information is available on A. seyal gum. In this study, we discovered a novel GH39 β-arabino-oligosaccharide 3-O-β-l-arabinopyranosyl-α-l-arabinofuranosidase from Bifidobacterium catenulatum and revealed the accurate structure of β-l-arabino-oligosaccharides released from A. seyal gum as [β-l-Araf-(1→2)-]n-β-l-Arap-(1→3)-α-l-Araf-(1→) (n = 0-3). Growth assays and intracellular enzyme activity assessments using B. catenulatum revealed that β-l-arabino-oligosaccharides were degraded to l-arabinose by GH127 β-l-arabinofuranosidase and GH36 β-l-arabinopyranosidase. This study provides new insights into the diversity of AGP structures and the utilization mechanisms of A. seyal gum in bifidobacteria.

Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species

Adult human facial skin microbiomes are remarkably similar at the species-level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 360 metagenomes, we reconstruct on-person evolutionary history to reveal on and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.

Bacterial Nanovesicles as Interkingdom Signaling Moieties Mediating Pain Hypersensitivity

Gut dysbiosis contributes to multiple pathologies, yet the mechanisms of the gut microbiota-mediated influence on systemic and distant responses remain largely elusive. This study aimed to identify the role of nanosized bacterial extracellular vesicles (bEVs) in mediating allodynia, i.e., pain hypersensitivity, in a diet-induced obesity (DIO) gut dysbiosis model. bEVs were enriched from the feces of lean (bEVLean) and DIO (bEVDIO) mice by an approach combining ultracentrifugation and immunoprecipitation and then extensively analyzed for purity and bacterial characteristics. Next, bEVs were injected, either intraplantarly or intravenously, in mice to assess pain sensitivity. Fluorescence-labeled bEVs were injected in mice by enema to assess biodistribution. The effect of bEV on immune cells and inflammation was analyzed by array, immunophenotyping, microscopy, NF-κB activation, and cellular uptake assays. Results showed that bEVDIO administration in wild-type mice replicated the allodynia phenotype observed in DIO mice for both mechanical and thermal stimuli. Importantly, this effect was compromised in TRPA1/TRPV1 double-knockout mice. Biodistribution analyses showed bEV entry into systemic circulation with subsequent localization at distant sites. Multiple analyses revealed that bEVDIO exposure incited systemic inflammation, primarily through modulating the innate immune system. This inflammatory mechanism involved LPS on the bEV surface, activating TLR2- and TLR4-related pathways, as confirmed using TLR2 and TLR4 inhibitors and shaving bEV surface proteins. Interestingly, the enhanced cellular uptake of bEVDIO was contingent on interactions involving LPS and proteins on bEVs and TLR2/TLR4 on monocytes. These findings illuminate the hitherto unexplored role of bEV as pivotal mediators of allodynia and inflammation linked to gut dysbiosis.

Gut microbiome composition in patients with liver cirrhosis with and without hepatic encephalopathy: A systematic review and meta-analysis

BACKGROUND

The gut microbiome is associated with hepatic encephalopathy (HE), but research results on the gut microbiome characteristics of patients with liver cirrhosis with and without HE are inconsistent.

AIM

To study the gut microbiota characteristics of patients with liver cirrhosis with and without HE.

METHODS

We searched the PubMed, Web of Science, EMBASE, and Cochrane databases using two keywords, HE, and gut microbiome. According to the inclusion and exclusion criteria, suitable literature was screened to extract data on the diversity and composition of the fecal microbiota in patients with liver cirrhosis with and without HE. The data were analyzed using RevMan and STATA.

RESULTS

Seventeen studies were included: (1) A meta-analysis of 7 studies revealed that the Shannon index in liver cirrhosis patients with HE was significantly lower than that in patients without HE [-0.20, 95% confidence interval (CI): -0.28 to -0.13, I2 = 20%]; (2) The relative abundances of Lachnospiraceae (-2.73, 95%CI: -4.58 to -0.87, I2 = 38%) and Ruminococcaceae (-2.93, 95%CI: -4.29 to -1.56, I2 = 0%) in liver cirrhosis patients with HE was significantly lower than those in patients without HE; (3) In patients with HE, Enterococcus, Proteobacteria, Enterococcaceae, and Enterobacteriaceae proportions increased, but Ruminococcaceae, Lachnospiraceae, Prevotellaceae, and Bacteroidetes proportions decreased; (4) Differences in the fecal metabolome between liver cirrhosis patients with and without HE were detected; and (5) Differential gut microbiomes may serve as diagnostic and prognostic tools.

CONCLUSION

The gut microbiomes of patients with liver cirrhosis with and without HE differ. Some gut microbiomes may distinguish liver cirrhosis patients with or without HE and determine patient prognosis.

Vibrio cholerae Gut Colonization of Zebrafish Larvae Induces a Dampened Sensorimotor Response

Background: Cholera is a diarrheal disease prevalent in populations without access to clean water. Cholera is caused by Vibrio cholerae, which colonizes the upper small intestine in humans once ingested. A growing number of studies suggest that the gut microbiome composition modulates animal behavior. Zebrafish are an established cholera model that can maintain a complex, mature gut microbiome during infection. Larval zebrafish, which have immature gut microbiomes, provide the advantage of high-throughput analyses for established behavioral models. Methods: We identified the effects of V. cholerae O1 El Tor C6706 colonization at 5 days post-fertilization (dpf) on larval zebrafish behavior by tracking startle responses at 10 dpf. We also characterized the larval gut microbiome using 16S rRNA sequencing. V. cholerae-infected or uninfected control groups were exposed to either an alternating light/dark stimuli or a single-tap stimulus, and average distance and velocity were tracked. Results: While there was no significant difference in the light/dark trial, we report a significant decrease in distance moved for C6706-colonized larvae during the single-tap trial. Conclusion: This suggests that early V. cholerae colonization of the larval gut microbiome has a dampening effect on sensorimotor function, supporting the idea of a link between the gut microbiome and behavior.

Dysbiosis-NK Cell Crosstalk in Pancreatic Cancer: Toward a Unified Biomarker Signature for Improved Clinical Outcomes

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis, primarily due to its immunosuppressive tumor microenvironment (TME), which contributes to treatment resistance. Recent research shows that the microbiome, including microbial communities in the oral cavity, gut, bile duct, and intratumoral environments, plays a key role in PDAC development, with microbial imbalances (dysbiosis) promoting inflammation, cancer progression, therapy resistance, and treatment side effects. Microbial metabolites can also affect immune cells, especially natural killer (NK) cells, which are vital for tumor surveillance, therapy response and treatment-related side effects. Dysbiosis can affect NK cell function, leading to resistance and side effects. We propose that a combined biomarker approach, integrating microbiome composition and NK cell profiles, can help predict treatment resistance and side effects, enabling more personalized therapies. This review examines how dysbiosis contributes to NK cell dysfunction in PDAC and discusses strategies (e.g., antibiotics, probiotics, vaccines) to modulate the microbiome and enhance NK cell function. Targeting dysbiosis could modulate NK cell activity, improve the effectiveness of PDAC treatments, and reduce side effects. However, further research is needed to develop unified NK cell-microbiome interaction-based biomarkers for more precise and effective patient outcomes.

Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology

Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.

How Do Microbial Metabolites Interact with Their Protein Targets?

The design of drugs and nutraceutics that mimic microbial metabolites is an emerging drug modality in medicinal chemistry that attempts to modulate the myriad of interactions that these molecules establish with host and microbial proteins. Understanding how microbial metabolites interact with their target proteins is key to perform a rational design of metabolite mimetic molecules for therapeutic usage. In the present work, we address this question by analyzing the functional groups of these molecules and the interactions they display in a set of more than 71K protein-metabolite interactions from the PDB. Significant differences in the functional group distributions, their chemical features, and their co-occurrences are observed for distinct subsets of these molecules. The same is true for the distributions of interaction types. By correlating both data sets, we are able to explain the observed interaction patterns in terms of observed functional group patterns. These results will shed light on the rational design of novel metabolite mimetic molecules for therapeutic purposes.

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative abundances of taxa and genes, they do not provide information on their absolute abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applying our prediction model to a large-scale metagenomic dataset (n = 34,539), we demonstrated that microbial load is the major determinant of gut microbiome variation and is associated with numerous host factors, including age, diet, and medication. We further found that for several diseases, changes in microbial load, rather than the disease condition itself, more strongly explained alterations in patients' gut microbiome. Adjusting for this effect substantially reduced the statistical significance of the majority of disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.

Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review

Immunotherapy, especially immune checkpoint inhibitor (ICI) therapy, has yielded remarkable outcomes for some patients with solid cancers, but others do not respond to these treatments. Recent research has identified the gut microbiota as a key modulator of immune responses, suggesting that its composition is closely linked to responses to ICI therapy in cancer treatment. As a result, the gut microbiome is gaining attention as a potential biomarker for predicting individual responses to ICI therapy and as a target for enhancing treatment efficacy. In this review, we discuss key findings from human observational studies assessing the effect of antibiotic use prior to ICI therapy on outcomes and identifying specific gut bacteria associated with favorable and unfavorable responses. Moreover, we review studies investigating the possibility of patient outcome prediction using machine learning models based on gut microbiome data before starting ICI therapy and clinical trials exploring whether gut microbiota modulation, for example via fecal microbiota transplantation or live biotherapeutic products, can improve results of ICI therapy in patients with cancer. We also briefly discuss the mechanisms through which the gut microbial-derived products influence immunotherapy effectiveness. Further research is necessary to fully understand the complex interactions between the host, gut microbiota, and immunotherapy and to develop personalized strategies that optimize responses to ICI therapy.

Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs

Shifts in host-associated microbiomes can impact both host and microbes.1,2,3,4,5,6 It is of interest to understand how perturbations, like the introduction of exogenous chemicals,7,8,9,10,11,12,13 impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.14,15,16,17,18,19 These alkaloids are antimicrobial20,21,22; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.

Comparative analysis of gut microbiota in major depressive disorder and schizophrenia during hospitalisation - the case-control, post hoc study

The aim of this study was to investigate the relationship between gut microbiota and major depressive disorder (MDD) and schizophrenia (SCZ) by comparing 36 inpatients with these conditions to 29 healthy controls (HC) matched for age, sex, and body mass index (BMI). Individuals with SCZ exhibited greater microbiota richness compared to HC (FDR P(Q)=0.028). Taxonomically, while no significant differences were observed between the microbiota of MDD and SCZ patients in a head-to-head comparison, both patient groups differed significantly when compared to HC. Interestingly, besides common patterns (such as a higher abundance of Erysipelotrichaceae UCG-003 and Streptococcus, and a lower abundance of Lachnospiraceae ND3007 group), unique patterns were exhibited only in MDD (with a higher abundance of Anaerostipes, Q=0.004) or SCZ (with a higher abundance of Sutterella, Q=0.001, and a lower abundance of Clostridium sensu stricto 1, Q=0.002). The Random Forest algorithm identified Ruminococcus torques group, Lachnospiraceae UCG-001, and Erysipelotrichaceae UCG-003 as highly discriminative features for both SCZ and MDD, while Suturella and Holdemania were unique features for SZC, and Lachnospiraceae genus CAG-56 and Anaerostipes for MDD. Additionally, between 50 % and 60 % of the differentially abundant taxa were found among the top 10 influential features in the RF models. In conclusion, while no significant differences were found between the microbiota of MDD and SCZ patients, distinct microbial patterns were found in each group when compared to HC. The study did not confirm universal microbial biomarkers reported in other studies but showed that the observed differences concern the bacteria associated with inflammation, the production of short chain fatty acids (SCFA), and the synthesis of metabolites linked to mental health (lactic acid, gamma-aminobutyric acid - GABA). The application of machine learning holds promise for further understanding the complex relationship between microbiota and these psychiatric disorders. The observed results should be treated with caution due to the limitations of this study (mainly sample size), therefore further researches under standardized environmental conditions with consistent analytical and bioinformatics approaches are warranted.

Unveiling gut microbiota's role: Bidirectional regulation of drug transport for improved safety

Drug safety is a paramount concern in the field of drug development, with researchers increasingly focusing on the bidirectional regulation of gut microbiota in this context. The gut microbiota plays a crucial role in maintaining drug safety. It can influence drug transport processes in the body through various mechanisms, thereby modulating their efficacy and toxicity. The main mechanisms include: (1) The gut microbiota directly interacts with drugs, altering their chemical structure to reduce toxicity and enhance efficacy, thereby impacting drug transport mechanisms, drugs can also change the structure and abundance of gut bacteria; (2) bidirectional regulation of intestinal barrier permeability by gut microbiota, promoting the absorption of nontoxic drugs and inhibiting the absorption of toxic components; (3) bidirectional regulation of the expression and activity of transport proteins by gut microbiota, selectively promoting the absorption of effective components or inhibiting the absorption of toxic components. This bidirectional regulatory role enables the gut microbiota to play a key role in maintaining drug balance in the body and reducing adverse reactions. Understanding these regulatory mechanisms sheds light on novel approaches to minimize toxic side effects, enhance drug efficacy, and ultimately improve drug safety. This review systematically examines the bidirectional regulation of gut microbiota in drug transportation from the aforementioned aspects, emphasizing their significance in ensuring drug safety. Furthermore, it offers a prospective outlook from the standpoint of enhancing therapeutic efficacy and reducing drug toxicity, underscoring the importance of further exploration in this research domain. It aims to provide more effective strategies for drug development and treatment.

Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges

BACKGROUND

In recent years, human microbiome research has flourished and has drawn attention from both healthcare professionals and general consumers as the human microbiome is now recognized as having a significant influence on human health. This has led to the emergence of companies offering microbiome testing services. Some of these services are sold directly to the consumer via companies' websites or via medical laboratory websites.

METHODOLOGY

In order to provide an overview of the consumer experience proposed by these microbiome testing services, one single faecal sample was sent to six different companies (five based in Europe and one based in the USA). Two out of the six testing kits were commercialized by medical laboratories, but without any requirement for a medical prescription. The analyses and reports received were discussed with a panel of experts (21 experts from 8 countries) during an online workshop.

RESULTS

This workshop led to the identification of several limitations and challenges related to these kits, including over-promising messages from the companies, a lack of transparency in the methodology used for the analysis and a lack of reliability of the results. The experts considered the interpretations and recommendations provided in the different reports to be premature due to the lack of robust scientific evidence and the analyses associated with the reports to be of limited clinical utility. The experts also discussed the grey areas surrounding the regulatory status of these test kits, including their positioning in the European market. The experts recommended a distinction between regulatory requirements based on the intended use or purpose of the kit: on the one hand, test kits developed to satisfy consumer curiosity, with a clear mention of this objective, and no mention of any disease or risk of disease, and on the other hand, in vitro diagnostic (IVD) CE-marked test kits, which could go deeper into the analysis and interpretation of samples, as such a report would be intended for trained healthcare professionals.

CONCLUSIONS

Recommendations or actions, specific to the context of use of microbiome testing kits, are listed to improve the quality and the robustness of these test kits to meet expectations of end users (consumers, patients and healthcare professionals). The need for standardization, robust scientific evidence, qualification of microbiome-based biomarkers and a clear regulatory status in Europe are the main issues that will require attention in the near future to align laboratory development with societal needs and thus foster translation into daily health practice.

Dynamic principles of the microbiome and the bovine vagina: a review

The role of microbes inhabiting various body sites in supporting host physiology and health is substantial, and recent advancements in DNA sequencing technology have facilitated a more in-depth understanding of these microbial contributions. The influence of microbiota within a given organ can be broadly categorized as having two main functions: (1) promoting organ homeostasis and (2) creating conditions that inhibit the growth of pathogenic microorganisms, thereby protecting the host from diseases. In livestock production, numerous phenotypes critical to industry outcomes are affected by the microbiome, which has sparked considerable academic interest in recent years. This review aims to analyze the extensive data available on the microbiomes of humans and other mammalian species, examining microbiome ecology to elucidate principles that may assist in interpreting data on livestock microbiomes. Additionally, the review will discuss techniques available for investigating various microbiome aspects and will examine existing data on the reproductive microbiome, with a particular focus on the bovine vaginal microbiome.

Mendelian randomization reveals predictive, preventive, and personalized insights into inflammatory bowel disease: the role of gut microbiome and circulating inflammatory proteins

Background

A chronic illness with increasing global frequency, inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), profoundly affects patients' quality of life and healthcare systems. IBD pathogenesis consists of changes in gut microbiota, immune system dysregulation, and genetic predisposition. Although emerging data suggests that gut microbiota and circulating inflammatory proteins play critical roles in IBD, their utility as biomarkers for predictive, preventive, and personalized medicine (PPPM) remains incompletely understood.

Working hypothesis and methods

We hypothesized that specific gut microbiota and inflammatory proteins causally influence IBD risk and mediate pathways between gut microbiota and IBD development. We employed Mendelian randomization (MR) using genome-wide association studies (GWAS) to explore these causal relationships, including further analyses on UC and CD subtypes.

Results

We identified eight gut microbiota species linked to IBD, with four protective and four increasing risk. Nine inflammatory proteins were also associated, six increasing risk and three protective. MMP-10 and IL-10Rα mediated the effects of Clostridiaceae1 on IBD risk. For UC, five microbiota species were protective, five were risk factors, and two proteins increased risk while three were protective. IL-10Rα mediated the effects of Clostridiaceae1 on UC risk. For CD, eight microbiota species were protective, four increased risk, and nine proteins were implicated. However, no mediation pathways were supported by multivariable MR.

Conclusions

This study highlights specific gut microbiota and inflammatory proteins that may serve as therapeutic targets for PPPM in IBD, UC, and CD. These findings offer new insights into IBD pathogenesis and suggest potential avenues for improved prevention, early detection, and personalized treatment strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-024-00384-2.

The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome

The gut microbiome plays a critical role to all animals and humans health. Methods based on ex vivo cultures are time and cost-effective solutions for rapid evaluation of probiotic effects on microbiomes. In this study, we assessed whether the protein secretome from the potential probiotic Enterococcus durans LAB18S grown on fructoligosaccharides (FOS) and galactoligosaccharides (GOS) had specific effects on ex vivo cultured intestinal microbiome obtained from a healthy individual. Metaproteomics was used to evaluate changes in microbial communities of the human intestinal microbiome. Hierarchical clustering analysis revealed 654 differentially abundant proteins from the metaproteome samples, showing that gut microbial protein expression varied on the presence of different E. durans secretomes. Increased amount of Bacteroidetes phylum was observed in treatments with secretomes from E. durans cultures on FOS, GOS and albumin, resulting in a decrease of the Firmicutes to Bacteroidetes (F/B) ratio. The most functionally abundant bacterial taxa were Roseburia, Bacteroides, Alistipes and Faecalibacterium. The results suggest that the secretome of E. durans may have favorable effects on the intestinal microbial composition, stimulating growth and different protein expression of beneficial bacteria. These findings suggest that proteins secreted by E. durans growing on FOS and GOS have different effects on the modulation of gut microbiota functional activities during cultivation.

Fecal microbiota transplantation validates the importance of gut microbiota in an ApoE-/- mouse model of chronic apical periodontitis-induced atherosclerosis

BACKGROUND

Chronic apical periodontitis (CAP) has been linked to the development of atherosclerosis, although the underlying mechanisms remain unclear. This study aimed to investigate the role of gut microbiota disruption in CAP-induced atherosclerosis development, focusing on trimethylamine N-oxide (TMAO)-related metabolites.

METHODS

The study utilized fecal microbiota transplantation (FMT) to transfer gut microbiota from mice with CAP to healthy mice. Atherosclerosis development was assessed by analyzing lesions in the aortic arch and aortic root. Serum lipid and inflammatory factor levels were measured. Composition and diversity of gut microbiota were analyzed using targeted metabolomics, with a focus on the ratio of Firmicutes to Bacteroidetes. The expression of hepatic flavin-containing monooxygenase 3 (FMO3) and serum TMAO levels were also evaluated.

RESULTS

Mice receiving gut microbiota from CAP mice showed increased atherosclerotic lesions compared to controls, without significant differences in serum lipid or inflammatory factor levels. Alterations in gut microbiota composition were observed, characterized by an increase in the Firmicutes to Bacteroidetes ratio. Peptostreptococcaceae abundance positively correlated with atherosclerosis severity, while Odoribacteraceae showed a negative correlation. No significant differences were found in hepatic FMO3 expression or serum TMAO levels.

CONCLUSIONS

The study confirms the role of gut microbiota disruption in CAP-mediated atherosclerosis development, independent of serum lipid or TMAO levels. Alterations in gut microbiota composition, particularly increased Firmicutes to Bacteroidetes ratio and specific bacterial families, were associated with atherosclerosis severity. These findings highlight the intricate interplay between gut microbiota and cardiovascular health in the context of CAP.

Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids

Keloid scarring is a fibroproliferative disease of the skin, which can significantly impact one's quality of life through cosmetic concerns, physical discomfort (itchy; painful), restricted movement, and psychological distress. Owing to the poorly understood pathogenesis of keloids and their high recurrence rate, the efficacy of keloid treatment remains unsatisfactory, particularly in patients susceptible to multiple keloids. We conducted fecal metagenomic analyzes and both untargeted and targeted plasma metabolomics in patients with multiple keloids (MK, n = 56) and controls with normal scars (NS, n = 60); tissue-untargeted metabolomics (MK, n = 35; NS, n = 32), tissue-targeted metabolomics (MK, n = 41; NS, n = 36), and single-cell sequencing analyzes (GSE163973). Differences in the gut microbiota composition, plasma metabolites, and tissue metabolites were observed between the MK and NS groups; the core gut microbiota, Oxalobacter formigenes, Bacteroides plebeius, and Parabacteroides distasonis, were identified via the gut microbiome co-occurrence network. Single-cell data helped clarify the specific cells affected by plasma metabolites. An area under the curve analysis using a random forest model based on fecal metagenomics, plasma metabolomics, and tissue metabolomics revealed that gut bacteria, plasma, and tissue metabolites were effective in distinguishing between MK and NS groups. Decreased Bacteroides plebeius could lower uracil levels, altering systemic lipid metabolism, which may change the metabolic phenotype of secretory reticular fibroblasts in wounds, potentially leading to MK. These findings may open new avenues for understanding the multifactorial nature of keloid formation from the gut-skin axis and highlight the potential for novel therapeutic strategies targeting keloid lesions and the underlying systemic imbalances affected by the gut microbiome.

Acupuncture and Moxibustion for Inflammatory Bowel Disease: Regulatory Mechanisms Revealed by Microbiome and Metabolomic Analysis

Acupuncture and moxibustion are widely acknowledged as effective complementary therapies for managing inflammatory bowel disease (IBD) in traditional Chinese medicine. However, the regulatory mechanisms by which these two therapies exert their therapeutic effects in IBD are yet to be fully elucidated. The objective of this study was to investigate the mechanisms of action underlying acupuncture and moxibustion and the regulative differences between them as therapeutic interventions for IBD. Using a dextran sodium sulfate-induced IBD mice model, the effects of the two treatments were evaluated by examination of body weight, stool samples, colon morphology, inflammatory factors, gut microbiota, and metabolites. The results indicated that both acupuncture and moxibustion mitigated body weight reduction; improved the structural characteristics of intestinal tissues; increased levels of anti-inflammatory cytokines including interleukin (IL)-10; and decreased levels of pro-inflammatory cytokines, including tumor necrosis factor-alpha (TNF-[Formula: see text]), nuclear factor kappa B (NF-[Formula: see text]B), IL-6, IL-1[Formula: see text], and IL-17. Acupuncture and moxibustion had distinct effects on the regulation of the intestinal microbiota and metabolic pathways in IBD mice. Moxibustion regulated a greater number of metabolic pathways than acupuncture, the majority of which were associated with amino acid metabolism, brain signal transmission, energy metabolism, and anti-inflammatory pathways. These findings provide a scientific basis for the differential applications of acupuncture and moxibustion in clinical practice.

Alteration of the Gut-Lung Axis After Severe COVID-19 Infection and Modulation Through Probiotics: A Randomized, Controlled Pilot Study

BACKGROUND

The gut-lung axis could be a potential therapeutic target for improving post-acute COVID-19 symptoms, and probiotics have been proposed as possible modulators.

AIM

We conducted a pilot study to understand alterations in the gut-lung axis and to explore the effects of a probiotic in post-acute COVID-19 disease.

METHODS

We included patients after severe COVID-19 disease (sCOV, n = 21) in a randomized, placebo-controlled trial to test the effect of a probiotic (Pro-Vi 5, Institute Allergosan, Graz, Austria) in a six-month intervention and used patients after mild disease (mCOV, n = 10) as controls, to compare the intestinal microbiome, metabolome, and patient-reported outcomes and biomarkers along the gut-lung axis at baseline and throughout probiotic intervention.

RESULTS

Compared to mCOV patients, sCOV patients showed lower microbial richness, which was significantly improved by probiotic intervention. A reorganization of Ruminococcaceae and Lachnospiraceae taxa was observed in sCOV patients but remained unaffected by the intervention. Serum metabolome showed a dysregulation of lipoproteins in accordance with higher BMI and comorbidities in sCOV patients. HDL and LDL fractions/components were temporarily decreased in the probiotic group. Stool metabolome was altered at baseline in sCOV patients and an increase in L-DOPA after 3 months and butyrate after 6 months of intervention could be observed. Probiotics partially improved reduced quality of life and modulated altered immune responses in sCOV patients. Increased intestinal permeability at baseline remained unaffected.

CONCLUSION

The study provides evidence of long-term alterations of the gut-lung axis after severe COVID-19 infection and suggests that probiotics can modulate the biomarkers of the gut-lung axis.

Gut microbiota and metabolomics unveil the mechanisms of Lomatogonium rotatum in ameliorating visceral fat and serum lipids in high-fat diet-induced obese mice

Lomatogonium rotatum (LR) is a folk medicinal herb traditionally used as a lipid-lowering and anti-obesity agent; but its pharmacological mechanism is unclear. In this study, we assessed the alterations of LR on gut microbes and serum metabolites in obese mice and their associated mechanisms of modulation on visceral fat and serum lipid by integrating gut microbiota and metabolomics analyses. Mice were fed a high-fat diet (HFD) to generate obesity and were then given LR and Orlistat orally at different doses (0.18, 0.9, 1.8 g/kg for LR and 0.048 g/kg for Orlistat) for a duration of 9 weeks. The impact of LR on weight loss was assessed through the examination of fat deposition, serum lipid indices, liver indices, and HE pathohistology. The effects of LR on gut microbiota and serum metabolites in obese mice were then investigated by 16S rRNA sequencing technology and untargeted metabolomics, and correlation analysis was performed. LR significantly reduced body weight, feed intake, Lee's index, visceral fat accumulation, serum TG, TC, AST and ALT, and elevated serum HDL levels in obese mice. In addition, 16S rRNA sequencing results indicated that the LR intervention remodeled microbial diversity and composition, increased the relative abundance of gut microbes Bacteroidetes and Porphyromonadaceae in HFD-induced obese mice, and decreased the Deferribacteres, Firmicutes and the Firmicutes/Bacteroidetes ratio. Correlation analyses showed that LR regulation of L-tyrosine and hesperetin metabolism, as well as alterations in the metabolic pathways of Phenylalanine, tyrosine and tryptophan biosynthesis, were associated with the changes in abundance of Bacteroidetes, Firmicutes, Porphyromonadaceae and Deferribacteres. Our study demonstrated that LR has lipid lowering and visceral fat reduction effects and its function may be closely related to the improvement of the gut microbiota and its associated metabolites.

Holistic Evaluation of the Gut Microbiota through Data Envelopment Analysis: A Cross-Sectional Study

Background

The gut microbiome plays a crucial role in human health, but maintaining a healthy gut microbiome remains challenging. Current approaches often focus on individual components rather than providing a holistic assessment.

Objectives

To introduce and evaluate a novel approach using data envelopment analysis (DEA) for assessing gut microbiota efficiency and identifying potential targets for personalized interventions.

Methods

We conducted a cross-sectional analysis of 577 participants from the Kanagawa "ME-BYO" Prospective Cohort Study. Lifestyle factors and gut microbiota composition were assessed. DEA was employed to calculate an efficiency score for each participant, incorporating multiple inputs (lifestyle factors) and outputs (gut microbiotas). This score represents how efficiently an individual's lifestyle factors contribute to their gut microbiota composition. Tobit regression analysis was used to assess associations between efficiency scores and demographic and health-related factors.

Results

The mean efficiency score was 0.86, with 14.2% of participants classified as efficient. Efficiency scores showed positive correlations with alcohol intake and Faith's phylogenetic diversity. Tobit regression analysis revealed significant associations between efficiency scores and sex, fat intake, and yogurt consumption. DEA identified specific targets for improving gut microbiota composition in inefficient individuals.

Conclusions

This study demonstrates the potential of DEA as a tool for evaluating gut microbiota efficiency and providing personalized recommendations for microbiota optimization. This approach could lead to more effective strategies for optimizing gut health across diverse populations.

The role of early life factors and green living environment in the development of gut microbiota in infancy: Population-based cohort study

OBJECTIVE

Early life microbial exposure influences the composition of gut microbiota. We investigated how early life factors, and the green living environment around infants' homes, influence the development of gut microbiota during infancy by utilizing data from the Steps to Healthy Development follow-up study (the STEPS study).

METHODS

The gut microbiota was analyzed at early (∼3 months, n = 959), and late infancy (∼13 months, n = 984) using 16S rRNA amplicon sequencing, and combined with residential green environment, measured as (1) Normalized Difference Vegetation Index, (2) Vegetation Cover Diversity, and (3) Naturalness Index within a 750 m radius. We compared gut microbiota diversity and composition between early and late infancy, identified significant individual and family level early life factors influencing gut microbiota, and determined the role of the residential green environment measures on gut microbiota development.

RESULTS

Alpha diversity (t-test, p < 0.001) and beta diversity (PERMANOVA, R2 = 0.095, p < 0.001) differed between early and late infancy. Birth mode was the strongest contributor to the gut microbiota community composition in early infancy (PERMANOVA, R2 = 0.005, p < 0.01) and the presence of siblings in late infancy (PERMANOVA, R2 = 0.007, p < 0.01). Residential green environment showed no association with community composition, whereas time spend outdoors did (PERMANOVA, R2 = 0.002, p < 0.05). Measures of greenness displayed a statistically significant association with alpha diversity during early infancy, not during late infancy (glm, p < 0.05). In adjusted analysis, the associations remained only with the Naturalness Index, where higher human impact on living environment was associated with decreased species richness (glm, Observed richness, p < 0.05).

CONCLUSIONS

The role of the residential green environment to the infant gut microbiota is especially important in early infancy, however, other early life factors, such as birth mode and presence of sibling, had a more significant effect on the overall community composition.

Recombinant Lactiplantibacilllus plantarum modulate gut microbial diversity and function

BACKGROUND

Gut microbes are important regulators of host health and can also function as disease indicators. Lactiplantibacilllus plantarum(L. plantarum)used as express and delivery vaccines for mucosal immunity have been shown to activate specific immune responses in numerous studies.

RESULTS

The interaction between recombinant L. plantarum and the gut microbiota was investigated in this study. The results indicated a change in the amount of gut OTU by recombinant L. plantarum. Recombinant L. plantarum dramatically boosted the species diversity of gut bacteria based on the Shannon-Wiener index. Beta diversity analysis showed that microbial structure was changed by recombinant L. plantarum. Furthermore, recombinant NC8 L. plantarum expressing a fusion between the P14.5 protein of the African swine fever virus and IL-33 enhanced the functions of gut bacteria in metabolism and immune regulation. Increased levels of IgG and IgG1 in serum and sIgA in feces, as well as enrichment of CD4+ T cells and IgA+ B cells, indicated that the gut microbiota exerted an immunomodulatory role when mediated by recombinant L. plantarum.

CONCLUSIONS

These results revealed that recombinant L. plantarum exerted its potential role in the gut microbiota and gut immunity.These fndings contribute to a broader understanding and utilization of L. plantarum bacteria in various therapeutic applications.

The potential influence and intervention measures of gut microbiota on sperm: it is time to focus on testis-gut microbiota axis

As the global male infertility rate continues to rise, there is an urgent imperative to investigate the underlying causes of sustained deterioration in sperm quality. The gut microbiota emerges as a pivotal factor in host health regulation, with mounting evidence highlighting its dual influence on semen. This review underscores the interplay between the Testis-Gut microbiota axis and its consequential effects on sperm. Potential mechanisms driving the dual impact of gut microbiota on sperm encompass immune modulation, inflammatory responses mediated by endotoxins, oxidative stress, antioxidant defenses, gut microbiota-derived metabolites, epigenetic modifications, regulatory sex hormone signaling. Interventions such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and Traditional natural herbal extracts are hypothesized to rectify dysbiosis, offering avenues to modulate gut microbiota and enhance Spermatogenesis and motility. Future investigations should delve into elucidating the mechanisms and foundational principles governing the interaction between gut microbiota and sperm within the Testis-Gut microbiota Axis. Understanding and modulating the Testis-Gut microbiota Axis may yield novel therapeutic strategies to enhance male fertility and combat the global decline in sperm quality.

Optimization of a DNA extraction protocol for improving bacterial and fungal classification based on Nanopore sequencing

Ribosomal RNA gene amplicon sequencing is commonly used to evaluate microbiome profiles in health and disease and document the impact of interventional treatments. Nanopore sequencing is attractive since it can provide greater classification at the species level. However, optimized protocols to target marker genes for bacterial and fungal profiling are needed. To achieve an increased taxonomic resolution, we developed extraction and full-length amplicon PCR-based approaches using Nanopore sequencing. Three lysis conditions were applied to a mock microbial community, including known bacterial and fungal species: ZymoBIOMICS lysis buffer (ML) alone, incorporating bead-beating (MLB) or bead-beating plus MetaPolyzyme enzymatic treatment (MLBE). In profiling of bacteria in comparison to reference data, MLB had more statistically different bacterial phyla and genera than the other two conditions. In fungal profiling, MLB had a significant increase of Ascomycota and a decline of Basidiomycota, subsequently failing to detect Malassezia and Cryptococcus. Also, a principal coordinates analysis plot by the Bray-Curtis metric showed a significant difference among groups for bacterial (P=0.033) and fungal (P=0.012) profiles, highlighting the importance of understanding the biases present in pretreatment. Overall, microbial profiling and diversity analysis revealed that ML and MLBE are more similar than MLB for both bacteria and fungi; therefore, using this specific pipeline, bead-beating is not recommended for whole gene amplicon sequencing. However, ML alone was suggested as an optimal approach considering DNA yield, taxonomic classification, reagent cost and hands-on time. This could be an initial proof-of-concept study for simultaneous human bacterial and fungal microbiome studies.

Identification of age-associated microbial changes via long-read 16S sequencing

BACKGROUND

Age-related gut microbial changes have been widely investigated over the past decade. Most of the previous age-related microbiome studies were conducted on the Western population, and the short-read sequencing (e.g., 16S V4 or V3-V4 region) was the most common microbiota profiling method. We evaluated the gut compositional differences using the long-read sequencing approach (i.e., PacBio sequencing targeting the full-length V1-V9 regions) to enable a deeper taxonomic resolution and better characterize the gut microbiome of Singaporeans from different age groups.

RESULTS

A total of 83 research participants were included in this study. Although no significant differences were detected in alpha and beta diversity, our study demonstrated several bacterial taxa with abundances that were significantly different across age groups. With young individuals as the reference group, Eggerthella lenta and Bacteroides uniformis were found to be significantly altered in the middle-aged group, while Catenibacterium mitsuokai and Bacteroides plebeius were significantly altered in the elderly group. These age-related differences in the gut microbiome were associated with aberrations in several predicted functional pathways, including dysregulations of pathways related to lipopolysaccharide and tricarboxylic acid cycle in older adults.

CONCLUSIONS

The utilization of long-read sequencing facilitated the identification of species- and strain-level differences across age groups, which was challenging with the partial 16S rRNA sequencing approach. Nevertheless, replication studies are warranted to confirm our findings, and if confirmed, further in vitro and in vivo studies are crucial to better understand the impact of the altered levels of age-related bacterial taxa. Additionally, the modest performance of strain-level taxonomic classification using 16S-ITS-23S gene sequences, likely due to the limited depth of currently available alignment databases, highlights the need for optimization and refinement in curating these databases for the long-read sequencing approach.

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.

The effects of stress on gut virome: Implications on infectious disease and systemic disorders

The role of gut microbiota in health and disease is being thoroughly examined in various contexts, with a specific focus on the bacterial fraction due to its significant abundance. However, despite their lower abundance, viruses within the gut microbiota are gaining recognition for their crucial role in shaping the structure and function of the intestinal microbiota, with significant effects on the host as a whole, particularly the immune system. Similarly, environmental factors such as stress are key in modulating the host immune system, which in turn influences the composition of the gut virome and neurological functions through the bidirectional communication of the gut-brain axis. In this context, alterations in the host immune system due to stress and/or dysbiosis of the gut virome are critical factors in the development of both infectious and noninfectious diseases. The molecular mechanisms and correlation patterns between microbial species are not yet fully understood. This literature review seeks to explore the interconnected relationship between stress and the gut virome, with a focus on how this interaction is influenced by the host's immune system. We also discuss how disturbances in this finely balanced system can lead to the onset and/or progression of diseases.

Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study

BACKGROUND

Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders.

METHODS

In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n = 203), including participants from a distinct population with a different metagenomic isolation protocol.

RESULTS

The gut microbiome of the patients had a significantly different β-diversity, but not α-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive association with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use.

CONCLUSIONS

Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.

Robust prediction of colorectal cancer via gut microbiome 16S rRNA sequencing data

Introduction. The study addresses the challenge of utilizing human gut microbiome data for the early detection of colorectal cancer (CRC). The research emphasizes the potential of using machine learning techniques to analyze complex microbiome datasets, providing a non-invasive approach to identifying CRC-related microbial markers.Hypothesis/Gap Statement. The primary hypothesis is that a robust machine learning-based analysis of 16S rRNA microbiome data can identify specific microbial features that serve as effective biomarkers for CRC detection, overcoming the limitations of classical statistical models in high-dimensional settings.Aim. The primary objective of this study is to explore and validate the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for colorectal cancer (CRC) detection and progression. The focus is on developing a classifier that effectively predicts the presence of CRC and normal samples based on the analysis of three previously published faecal 16S rRNA sequencing datasets.Methodology. To achieve the aim, various machine learning techniques are employed, including random forest (RF), recursive feature elimination (RFE) and a robust correlation-based technique known as the fuzzy forest (FF). The study utilizes these methods to analyse the three datasets, comparing their performance in predicting CRC and normal samples. The emphasis is on identifying the most relevant microbial features (taxa) associated with CRC development via partial dependence plots, i.e. a machine learning tool focused on explainability, visualizing how a feature influences the predicted outcome.Results. The analysis of the three faecal 16S rRNA sequencing datasets reveals the consistent and superior predictive performance of the FF compared to the RF and RFE. Notably, FF proves effective in addressing the correlation problem when assessing the importance of microbial taxa in explaining the development of CRC. The results highlight the potential of the human microbiome as a non-invasive means to detect CRC and underscore the significance of employing FF for improved predictive accuracy.Conclusion. In conclusion, this study underscores the limitations of classical statistical techniques in handling high-dimensional information such as human microbiome data. The research demonstrates the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for CRC detection. Applying machine learning techniques, particularly the FF, is a promising approach for building a classifier to predict CRC and normal samples. The findings advocate for integrating FF to overcome the challenges associated with correlation when identifying crucial microbial features linked to CRC development.

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies

BACKGROUND

In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.

RESULTS

Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.

CONCLUSIONS

Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.

Microbiome signature suggestive of lactose-intolerance in rhesus macaques (Macaca mulatta) with intermittent chronic diarrhea

BACKGROUND

Chronic diarrhea is a common cause of mortality and morbidity in captive rhesus macaques (Macaca mulatta). The exact etiology of chronic diarrhea in macaques remains unidentified. The occurrence of diarrhea is frequently linked to dysbiosis within the gut microbiome. Research into microbiome signatures correlated with diarrhea in macaques have predominantly been conducted with single sample collections. Our analysis was based on the metagenomic composition of longitudinally acquired fecal samples from rhesus macaques with chronic diarrhea and clinically healthy rhesus macaques that were obtained over the course of two years. We aimed to investigate potential relationships between the macaque gut microbiome, the presence of diarrhea and diet interventions with a selection of commercially available monkey diets.

RESULTS

The microbiome signature of macaques with intermittent chronic diarrhea showed a significant increase in lactate producing bacteria e.g. lactobacilli, and an increase in fermenters of lactate and succinate. Strikingly, two lactose free diets were associated with a lower incidence of diarrhea.

CONCLUSION

A lactose intolerance mechanism is suggested in these animals by the bloom of Lactobacillus in the presence of lactose resulting in an overproduction of intermediate fermentation products likely led to osmotically induced diarrhea. This study provides new insights into suspected microbiome-lactose intolerance relationship in rhesus macaques with intermittent chronic diarrhea. The integration of machine learning with metagenomic data analysis holds potential for developing targeted dietary interventions and therapeutic strategies and therefore ensuring a healthier and more resilient primate population.

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.

Gut Microbiota and Probiotics in Perioperative Management: A Narrative Review

The human gut is the abode of several complex and diverse microbes. It is a fact that the human brain is interconnected with the spinal cord and sense organs; however, there is also a possibility of a connection between the brain and the gut microbiome. The human gut can be altered in various ways, the principal method being the intake of prebiotics, probiotics and synbiotics. Can this alteration in the gut microbiome be clinically utilised in the perioperative period? We conducted a literature search related to this topic using databases and search engines (Medical Literature Analysis and Retrieval System Online {MEDLINE}, Embase, Scopus, PubMed and Google Scholar). The search revealed some preclinical and clinical studies in animals and humans that demonstrate the alteration of the gut microbiome with the use of anxiolysis, probiotics/prebiotics and other perioperative factors including opioids, anaesthetics and perioperative stress. The significant effects of this alteration have been seen on preoperative anxiety and postoperative delirium/cognitive dysfunction/pain. These effects are described in this narrative review, which opens up newer vistas for high-quality research related to the gut microbiome, gut-brain axis, the related signaling pathways and their clinical application in the perioperative period.

Gut microbiome changes associated with chronic pancreatitis and pancreatic cancer: a systematic review and meta-analysis

BACKGROUND

The study of changes in the microbiome in chronic pancreatitis (CP) and pancreatic ductal adenocarcinoma (PDAC) holds significant potential for developing noninvasive diagnostic tools as well as innovative interventions to alter the progression of diseases. This systematic review and meta-analysis aimed to analyze in detail the taxonomic and functional characteristics of the gut microbiome in patients with CP and PDAC.

METHODS

Two researchers conducted a systematic search across public databases to gather all published research up to June 2023. Diversity and gut microbiota composition are the main outcomes the authors focus on.

RESULTS

This meta-analysis included 14 studies, involving a total of 1511 individuals in the PDAC ( n =285), CP ( n =342), and control ( n =649) groups. Our results show a significant difference in the composition of gut microbiota between PDAC/CP patients compared to healthy controls (HC), as evidenced by a slight decrease in α-diversity, including Shannon (SMD=-0.33; P =0.002 and SMD=-0.59; P <0.001, respectively) and a statistically significant β-diversity ( P <0.05). The pooled results showed that at the phylum level, the proportion of Firmicutes was lower in PDAC and CP patients than in HC patients. At the genus level, more than two studies demonstrated that four genera were significantly increased in PDAC patients compared to HC (e.g. Escherichia-Shigella and Veillonella ). CP patients had an increase in four genera (e.g. Escherichia-Shigella and Klebsiella ) and a decrease in eight genera (e.g. Coprococcus and Bifidobacterium ) compared to HC. Functional/metabolomics results from various studies also showed differences between PDAC/CP patients and HC. In addition, this study found no significant differences in gut microbiota between PDAC and CP patients.

CONCLUSIONS

Current evidence suggests changes in gut microbiota is associated with PDAC/CP, commonly reflected by a reduction in beneficial species and an increase in the pathogenic species. Further studies are needed to confirm these findings and explore therapeutic possibilities.

Gut-muscle axis mechanism of exercise prevention of sarcopenia

Sarcopenia refers to an age-related systemic skeletal muscle disorder, which is characterized by loss of muscle mass and weakening of muscle strength. Gut microbiota can affect skeletal muscle through a variety of mechanisms. Gut microbiota present distinct features among elderly people and sarcopenia patients, including a decrease in microbial diversity, which might be associated with the quality and function of the skeletal muscle. There might be a gut-muscle axis; where gut microbiota and skeletal muscle may affect each other bi-directionally. Skeletal muscle can affect the biodiversity of the gut microbiota, and the latter can, in turn, affect the anabolism of skeletal muscle. This review examines recent studies exploring the relationship between gut microbiota and skeletal muscle, summarizes the effects of exercise on gut microbiota, and discusses the possible mechanisms of the gut-muscle axis.

Activity-based metaproteomics driven discovery and enzymological characterization of potential α-galactosidases in the mouse gut microbiome

The gut microbiota offers an extensive resource of enzymes, but many remain uncharacterized. To distinguish the activities of similar annotated proteins and mine the potentially applicable ones in the microbiome, we applied an effective Activity-Based Metaproteomics (ABMP) strategy using a specific activity-based probe (ABP) to screen the entire gut microbiome for directly discovering active enzymes and their potential applications, not for exploring host-microbiome interactions. By using an activity-based cyclophellitol aziridine probe specific to α-galactosidases (AGAL), we successfully identified and characterized several gut microbiota enzymes possessing AGAL activities. Cryo-electron microscopy analysis of a newly characterized enzyme (AGLA5) revealed the covalent binding conformations between the AGAL5 active site and the cyclophellitol aziridine ABP, which could provide insights into the enzyme's catalytic mechanism. The four newly characterized AGALs have diverse potential activities, including raffinose family oligosaccharides (RFOs) hydrolysis and enzymatic blood group transformation. Collectively, we present a ABMP platform that facilitates gut microbiota AGALs discovery, biochemical activity annotations and potential industrial or biopharmaceutical applications.

Investigating the causal relationship between gut microbiota and gastroenteropancreatic neuroendocrine neoplasms: a bidirectional Mendelian randomization study

Background

The interaction between the intestinal flora and gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) remains poorly understood, despite the known effect of the gut microbiota on gastrointestinal adenocarcinomas. Hence, the present research aimed to determine the potential causal correlation between the intestinal flora and GEP-NENs by conducting a bidirectional Mendelian randomization (MR) analysis.

Methods

Two-sample MR analysis was conducted using the summary statistics of the gut microbiota from the MiBioGen consortium and those of GEP-NENs from the FinnGen research project. The inverse-variance weighted approach was utilized as the primary analytical method. To enhance the robustness of our findings, multiple sensitivity tests were performed, including Cochran's Q test for evaluating heterogeneity, the MR-Egger intercept test to detect horizontal pleiotropy, and the MR-PRESSO test to identify outliers and assess pleiotropy bias. Additionally, a leave-one-out analysis was performed to validate the consistency of our findings. The MR-Steiger test was also utilized to determine the causal direction in the correlation between the gut microbiota and GEP-NENs. Finally, a reverse MR analysis was performed to assess reverse causality between the intestinal flora and GEP-NENs.

Results

We identified 42 taxa of the gut microbiota that were potentially causally associated with GEP-NENs; of these taxa, 7, 8, 11, and 16 taxa were causally associated with pancreatic NENs, colorectal NENs, small intestinal NENs, and gastric NENs, respectively. After adjusting for false discovery rate (FDR) correction, we found significant causal links of Euryarchaeota with small intestinal NENs and Family XIII UCG-001 with gastric NENs. The sensitivity analyses confirmed the stability of these correlations. In the reverse MR analysis, colorectal NENs and small intestinal NENs were found to be associated with variations in 8 and 6 different taxa of the gut microbiota, respectively. After adjusting for FDR correction, no significant causal links were detected between GEP-NENs and the intestinal flora.

Conclusion

The present study reveals a potential causal association between certain taxa of the intestinal flora and GEP-NENs, thus providing new perspectives regarding the role of the intestinal flora in the development of these tumors. These insights could provide innovative approaches to screen and prevent these diseases.

The gut microbiota-brain axis in neurological disorders

Previous studies have shown a bidirectional communication between human gut microbiota and the brain, known as the microbiota-gut-brain axis (MGBA). The MGBA influences the host's nervous system development, emotional regulation, and cognitive function through neurotransmitters, immune modulation, and metabolic pathways. Factors like diet, lifestyle, genetics, and environment shape the gut microbiota composition together. Most research have explored how gut microbiota regulates host physiology and its potential in preventing and treating neurological disorders. However, the individual heterogeneity of gut microbiota, strains playing a dominant role in neurological diseases, and the interactions of these microbial metabolites with the central/peripheral nervous systems still need exploration. This review summarizes the potential role of gut microbiota in driving neurodevelopmental disorders (autism spectrum disorder and attention deficit/hyperactivity disorder), neurodegenerative diseases (Alzheimer's and Parkinson's disease), and mood disorders (anxiety and depression) in recent years and discusses the current clinical and preclinical gut microbe-based interventions, including dietary intervention, probiotics, prebiotics, and fecal microbiota transplantation. It also puts forward the current insufficient research on gut microbiota in neurological disorders and provides a framework for further research on neurological disorders.

Microecological regulation in HCC therapy: Gut microbiome enhances ICI treatment

The exploration of the complex mechanisms of cancer immunotherapy is rapidly evolving worldwide, and our focus is on the interaction of hepatocellular carcinoma (HCC) with immune checkpoint inhibitors (ICIs), particularly as it relates to the regulatory role of the gut microbiome. An important basis for the induction of immune responses in HCC is the presence of specific anti-tumor cells that can be activated and reinforced by ICIs, which is why the application of ICIs results in sustained tumor response rates in the majority of HCC patients. However, mechanisms of acquired resistance to immunotherapy in unresectable HCC result in no long-term benefit for some patients. The significant heterogeneity of inter-individual differences in the gut microbiome in response to treatment with ICIs makes it possible to target modulation of specific gut microbes to assist in augmenting checkpoint blockade therapies in HCC. This review focuses on the complex relationship between the gut microbiome, host immunity, and HCC, and emphasizes that manipulating the gut microbiome to improve response rates to cancer ICI therapy is a clinical strategy with unlimited potential.

Molecular Mechanisms behind Obesity and Their Potential Exploitation in Current and Future Therapy

Obesity is a chronic disease caused primarily by the imbalance between the amount of calories supplied to the body and energy expenditure. Not only does it deteriorate the quality of life, but most importantly it increases the risk of cardiovascular diseases and the development of type 2 diabetes mellitus, leading to reduced life expectancy. In this review, we would like to present the molecular pathomechanisms underlying obesity, which constitute the target points for the action of anti-obesity medications. These include the central nervous system, brain-gut-microbiome axis, gastrointestinal motility, and energy expenditure. A significant part of this article is dedicated to incretin-based drugs such as GLP-1 receptor agonists (e.g., liraglutide and semaglutide), as well as the brand new dual GLP-1 and GIP receptor agonist tirzepatide, all of which have become "block-buster" drugs due to their effectiveness in reducing body weight and beneficial effects on the patient's metabolic profile. Finally, this review article highlights newly designed molecules with the potential for future obesity management that are the subject of ongoing clinical trials.

The Role of the Gut and Airway Microbiota in Chronic Rhinosinusitis with Nasal Polyps: A Systematic Review

In recent years, there has been growing interest in understanding the potential role of microbiota dysbiosis or alterations in the composition and function of human microbiota in the development of chronic rhinosinusitis with nasal polyposis (CRSwNP). This systematic review evaluated the literature on CRSwNP and host microbiota for the last ten years, including mainly nasal bacteria, viruses, and fungi, following the PRISMA guidelines and using the major scientific publication databases. Seventy original papers, mainly from Asia and Europe, met the inclusion criteria, providing a comprehensive overview of the microbiota composition in CRSwNP patients and its implications for inflammatory processes in nasal polyps. This review also explores the potential impact of microbiota-modulating therapies for the CRSwNP treatment. Despite variability in study populations and methodologies, findings suggest that fluctuations in specific taxa abundance and reduced bacterial diversity can be accepted as critical factors influencing the onset or severity of CRSwNP. These microbiota alterations appear to be implicated in triggering cell-mediated immune responses, cytokine cascade changes, and defects in the epithelial barrier. Although further human studies are required, microbiota-modulating strategies could become integral to future combined CRSwNP treatments, complementing current therapies that mainly target inflammatory mediators and potentially improving patient outcomes.