Recent advances in modulating the microbiome

Effect of probiotics at different intervention time on glycemic control in patients with type 2 diabetes mellitus: a systematic review and meta-analysis

Background

Type 2 diabetes mellitus(T2DM) is characterized by hyperglycemia. Gut microbiome adjustment plays a positive part in glucose regulation, which has become a hotspot. Probiotics have been studied for their potential to control the gut flora and to treat T2DM. However, the conclusion of its glucose-lowering effect is inconsistent based on different probiotic intervention times.

Objectives

To comprehensively evaluate how various probiotic intervention times affect glycemic control in people with T2DM.

Methods

We retrieved PubMed, Embase, Web of Science, and Cochrane Library on randomized controlled trials(RCTs)regarding the impact of probiotics on glycemic control in patients with T2DM from the inception to November 16, 2023. Separately, two researchers conducted a literature analysis, data extraction, and bias risk assessment of the involved studies. We followed the PRISMA guidelines, used RevMan 5.4 software for meta-analysis, and assessed the risk of bias by applying the Cochrane Handbook for Systematic Reviews 5.1.0.

Results

We included eight RCTs with 507 patients. Meta-analysis revealed that the use of probiotics might considerably reduce levels of glycosylated hemoglobin (HbA1c) {mean deviation (MD) = -0.33, 95% confidence interval (CI) (-0.59, -0.07), p = 0.01}, Insulin {standard mean deviation (SMD) = -0.48, 95% CI (-0.74, -0.22), p = 0.0003} and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR){SMD = -1.36, 95% CI (-2.30, -0.41), p = 0.005} than placebo group. No statistically significant differences were found regarding fasting blood glucose (FBG) and body mass index (BMI) {SMD = -0.39, 95% CI (-0.83, 0.05), p = 0.08}, {SMD = -0.40, 95% CI (-1.07, 0.27), p = 0.25}, respectively. Subgroup analyses, grouped by intervention times, showed that six to eight weeks of intervention improved HbA1c compared to the control group (p < 0.05), both six to eight weeks and 12-24 weeks had a better intervention effect on Insulin, and HOMA-IR (p < 0.05).In contrast, there was no statistically significant variation in the length between FBG and BMI regarding duration.

Conclusion

This meta-analysis found probiotics at different intervention times play a positive role in modulating glucose in T2DM, specifically for HbA1c in six to eight weeks, Insulin and HOMA-IR in six to eight weeks, and 12-24 weeks. To confirm our findings, further excellent large-sample research is still required.

Systematic review registration

https://www.crd.york.ac.uk/prospero, identifier CRD42023483325.

A synbiotic mixture of Bifidobacterium breve M16-V, oligosaccharides and pectin, enhances Short Chain Fatty Acid production and improves lung health in a preclinical model for pulmonary neutrophilia

Introduction

Pulmonary neutrophilia is a hallmark of numerous airway diseases including Chronic Obstructive Pulmonary Disease (COPD), Neutrophilic asthma, Acute Lung Injury (ALI), Acute Respiratory Distress Syndrome (ARDS) and COVID-19. The aim of the current study was to investigate the effect of dietary interventions on lung health in context of pulmonary neutrophilia.

Methods

Male BALB/cByJ mice received 7 intra-nasal doses of either a vehicle or lipopolysaccharides (LPS). To study the effect of nutritional interventions they received 16 intra-gastric doses of either a vehicle (PBS) or the following supplements (1) probiotic Bifidobacterium breve (B. breve) M16-V; (2) a prebiotic fiber mixture of short-chain galacto-oligosaccharides, long-chain fructo-oligosaccharides, and low-viscosity pectin in a 9:1:2 ratio (scGOS/lcFOS/lvPectin); and (3) A synbiotic combination B. breve M16-V and scGOS/lcFOS/lvPectin. Parameters for lung health included lung function, lung morphology and lung inflammation. Parameters for systemic immunomodulation included levels of fecal short chain fatty acids and regulatory T cells.

Results

The synbiotic supplement protected against the LPS induced decline in lung function (35% improved lung resistance at baseline p = 0.0002 and 25% at peak challenge, p = 0.0002), provided a significant relief from pulmonary neutrophilia (40.7% less neutrophils, p < 0.01) and improved the pulmonary neutrophil-to-lymphocyte ratio (NLR) by 55.3% (p = 0.0033). Supplements did not impact lung morphology in this specific experiment. LPS applied to the upper airways induced less fecal SCFAs production compared to mice that received PBS. The production of acetic acid between day -5 and day 16 was increased in all unchallenged mice (PBS-PBS p = 0.0003; PBS-Pro p < 0.0001; PBS-Pre, p = 0.0045; PBS-Syn, p = 0.0005) which upon LPS challenge was only observed in mice that received the synbiotic mixture of B. breve M16-V and GOS:FOS:lvPectin (p = 0.0003). A moderate correlation was found for butyric acid and lung function parameters and a weak correlation was found between acetic acid, butyric acid and propionic acid concentrations and NLR.

Conclusion

This study suggests bidirectional gut lung cross-talk in a mouse model for pulmonary neutrophilia. Neutrophilic lung inflammation coexisted with attenuated levels of fecal SCFA. The beneficial effects of the synbiotic mixture of B. breve M16-V and GOS:FOS:lvPectin on lung health associated with enhanced levels of SCFAs.

The interaction between gut microbiome and bone health

PURPOSE OF REVIEW

This review critically examines interconnected health domains like gut microbiome, bone health, interleukins, chronic periodontitis, and coronavirus disease 2019 (COVID-19), offering insights into fundamental mechanisms and clinical implications, contributing significantly to healthcare and biomedical research.

RECENT FINDINGS

This review explores the relationship between gut microbiome and bone health, a growing area of study. It provides insights into skeletal integrity and potential therapeutic avenues. The review also examines interleukins, chronic periodontitis, and COVID-19, highlighting the complexity of viral susceptibility and immune responses. It highlights the importance of understanding genetic predispositions and immune dynamics in the context of disease outcomes. The review emphasizes experimental evidence and therapeutic strategies, aligning with evidence-based medicine and personalized interventions. This approach offers actionable insights for healthcare practitioners and researchers, paving the way for targeted therapeutic approaches and improved patient outcomes.

SUMMARY

The implications of these findings for clinical practice and research underscore the importance of a multidisciplinary approach to healthcare that considers the complex interactions between genetics, immune responses, oral health, and systemic diseases. By leveraging advances in biomedical research, clinicians can optimize patient care and improve health outcomes across diverse patient populations.

Application of Microbiome-Based Therapies in Chronic Respiratory Diseases

The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and affected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably different, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome influences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fiber diets, for example, present beneficial effects through the production of short-chain fatty acids. Additionally, genetically modified probiotics to secrete some beneficial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics

While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member Caenorhabditis elegans microbiome community comprising the immune-protective target species Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.IMPORTANCEWhile various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm Caenorhabditis elegans comprising the host-beneficial Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11 in vitro and in vivo. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.

The Effects of Oral Probiotics on Type 2 Diabetes Mellitus (T2DM): A Clinical Trial Systematic Literature Review

Type 2 diabetes mellitus (T2DM) remains a global health concern. Emerging clinical trial (CT) evidence suggests that probiotic intervention may promote a healthy gut microbiome in individuals with T2DM, thereby improving management of the disease. This systematic literature review summarizes thirty-three CTs investigating the use of oral probiotics for the management of T2DM. Here, twenty-one studies (64%) demonstrated an improvement in at least one glycemic parameter, while fifteen studies (45%) showed an improvement in at least one lipid parameter. However, no article in this review was able to establish a uniform decrease in glycemic, lipid, or blood pressure profiles. The lack of consistency across the studies may be attributed to differences in probiotic composition, duration of probiotic consumption, and probiotic dose. An interesting finding of this literature review was the beneficial trend of metformin and probiotic co-administration. Here, patients with T2DM taking metformin demonstrated enhanced glycemic control via the co-administration of probiotics. Taken together, the overall positive findings reported across the studies in combination with minimal adverse effects constitute ground for further quality CTs. This review provides recommendations for future CTs that may address the shortcomings of the current studies and help to extract useful data from future investigations of the use of probiotics in T2DM management.

A short-term bioreactor assay to assess the effect of essential oils on a microbiota derived from piglet's intestinal content

BACKGROUND

Modulating the microbiota is an emerging way to improve pig health. In-vitro bioreactor systems can be used to reproduce intestinal microbiota to study modulating avenues. In this study, a continuous feeding system to support a microbiota derived from piglet colonic contents, over 72 h, was developed. The microbiota from piglets was collected and used as inoculum. The culture media was derived from an artificial digestion of piglet feed. The microbiota diversity in time, the reproducibility between replicates and the diversity of the bioreactor microbiota compared to the inoculum was assessed. Essential oils were used as a proof of concept to assess the in vitro microbiota modulation. The microbiota diversity was assessed by 16S rRNA amplicon sequencing. Quantitative PCR was also used for total bacteria, lactobacilli and Enterobacteria.

RESULTS

At the start of the assay, the bioreactor microbiota diversity was similar to the inoculum. Time and replication affected the bioreactor microbiota diversity. Between 48 and 72 h, no statistical variation of the microbiota diversity was observable. After a 48 h running period, thymol and carvacrol were added at 200 ppm or 1000 ppm for 24 h. No microbiota modification was observed by sequencing. Quantitative PCR results showed a significant growth of lactobacilli when thymol was used at 1000 ppm, where only a trend was observed with the 16S analysis.

CONCLUSIONS

This study presents a bioreactor assay that can be used as a tool for rapid screening of additives and suggests that the effects of essential oils on the microbiota are subtle, acting against a few bacterial genera.

Effect of Antibiotic Eye Drops on the Nasal Microbiome in Healthy Subjects—A Pilot Study

Background: Antibiotic eye drops are frequently used in clinical practice. Due to the anatomical connection via the nasolacrimal duct, it seems possible that they have an influence on the nasal/pharyngeal microbiome. This was investigated by using two different commonly used antibiotic eye drops. Methods: 20 subjects were randomized to four groups of five subjects receiving eye drops containing gentamicin, ciprofloxacin, or, as controls, unpreserved povidone or benzalkonium chloride-preserved povidone. Nasal and pharyngeal swabs were performed before and after the instillation period. Swabs were analyzed by Illumina next-generation sequencing (NGS)-based 16S rRNA analysis. Bacterial culture was performed on solid media, and bacterial isolates were identified to the species level by MALDI-TOF MS. Species-dependent antimicrobial susceptibility testing was performed using single isolates and pools of isolates. Results: Bacterial richness in the nose increased numerically from 163 ± 30 to 243 ± 100 OTUs (gentamicin) and from 114 ± 17 to 144 ± 45 OTUs (ciprofloxacin). Phylogenetic diversity index (pd) of different bacterial strains in the nasal microbiome increased from 12.4 ± 1.0 to 16.9 ± 5.6 pd (gentamicin) and from 10.2 ± 1.4 to 11.8 ± 3.1 pd (ciprofloxacin). Unpreserved povidone eye drops resulted in minimal changes in bacterial counts. Preservative-containing povidone eye drops resulted in no change. A minor increase (1–2-fold) in the minimal inhibitory concentration (MIC) was observed in single streptococcal isolates. Conclusions: Antibiotic eye drops could affect the nasal microbiome. After an instillation period of seven days, an increase in the diversity and richness of bacterial strains in the nasal microbiome was observed.

Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics

The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, there is still a lack of approaches that allow to specifically modulate the abundance of individual microbes or microbial functions of interest. Moreover, current approaches for microbiome manipulation such as fecal transfers often entail a non-specific transfer of entire microbial communities with potentially unwanted side effects. To overcome this limitation, we here propose the concept of precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In a first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we present a metabolic modeling network framework that allows us to define precision prebiotics for a two-member C. elegans microbiome model community comprising the immune-protective Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. Thus, we predicted compounds that specifically boost the abundance of the host-beneficial MYb11, four of which were experimentally validated in vitro (L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid). L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that constraint-based metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.

The Role of Gut Dysbiosis and Potential Approaches to Target the Gut Microbiota in Multiple Sclerosis

It has now been established that a perturbation in gut microbiome composition exists in multiple sclerosis (MS) and its interplay with the immune system and brain could potentially contribute to the development of the disease and influence its course. The effects of the gut microbiota on the disease may be mediated by direct interactions between bacteria and immune cells or through interactions of products of bacterial metabolism with immune and CNS cells. In this review article we summarize the ways in which the gut microbiome of people with MS differs from controls and how bacterial metabolites can potentially play a role in MS pathogenesis, and examine approaches to alter the composition of the gut microbiota potentially alleviating gut dysbiosis and impacting the course of MS.

Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life

The development of infant gut microbiome is a pivotal process affecting the ecology and function of the microbiome, as well as host health. While the establishment of the infant microbiome has been of interest for decades, the focus on gut microbial metabolism and the resulting small molecules (metabolites) has been rather limited. However, technological and computational advances are now enabling researchers to profile the plethora of metabolites in the infant gut, allowing for improved understanding of how gut microbial-derived metabolites drive microbiome community structuring and host-microbial interactions. Here, we review the current knowledge on development of the infant gut microbiota and metabolism within the first year of life, and discuss how these microbial metabolites are key for enhancing our basic understanding of interactions during the early life developmental window.

Transfer efficiency and impact on disease phenotype of differing methods of gut microbiota transfer

To test causal relationships between complex gut microbiota (GM) and host outcomes, researchers frequently transfer GM between donor and recipient mice via embryo transfer (ET) rederivation, cross-fostering (CF), and co-housing. In this study, we assess the influence of the transfer method and the differences in baseline donor and recipient microbiota richness, on transfer efficiency. Additionally, recipient mice were subjected to DSS-induced chronic colitis to determine whether disease severity was affected by GM transfer efficiency or features within the GM. We found that the recipient's genetic background, the baseline richness of donor and recipient GM, and the transfer method all influenced the GM transfer efficiency. Recipient genetic background and GM both had significant effects on DSS colitis severity and, unexpectedly, the transfer method was strongly associated with differential disease severity regardless of the other factors.

Innovations for microbiome targeting interventions - a patent landscape analysis indicating overall patenting activity decline and promising target disease areas

The human microbiota have been implicated in the aetiology and remedy of a host of disorders. However, due to the pervasive uncertainty inherent in the field of microbiota-targeting interventions and associated issues with establishing rigorous safety and efficacy profiles, regulatory oversight is suboptimal. This can dissuade innovators from further exploring novel and much needed health interventions. Modification of regulatory protocols and practices requires focussed efforts and funding to build the evidence base around future regulatory needs. Such modification can be critically informed by identification of changes and trends in technology fields to facilitate identification of regulatory gaps. To this purpose, this study rigorously collected and analysed patent data from Espacenet - covering the years 2013-2018 - and created a patent landscape analysis of microbiome targeting interventions with a focus on medicinal products. Pertinent patenting activity has declined overall. While, in absolute terms, patents most frequently claimed inventions targeting disorders of the gut and alimentary tract, relative year-on-year interest increases have been substantial for cancer, and disorders of the (neuro-)muscular and respiratory systems - driven by the private sector. Academic stakeholders showed top interest in disorders of the metabolism, anti-infectives, and skeletal and dermatological diseases. Although medicinal preparation claims dominated our dataset, a third of patents claimed food preparations, while only 1% claimed application as a diagnostic. Finally, China is, by an inordinate margin, a market of particular interest for both domestic and foreign innovators, indicating that microbiome targeting intervention innovation for EU and US markets might be frustrated. This study is the first to empirically demonstrate that live biotherapeutic product innovation is decelerating and potentially frustrated, supporting the urgent need for improved regulatory standards. Our results indicate which disease areas deserve particular attention for research funding to facilitate proper regulatory appraisal in the near- to mid-term future.

Bile acids and their receptors: modulators and therapeutic targets in liver inflammation

Bile acids participate in the intestinal emulsion, digestion, and absorption of lipids and fat-soluble vitamins. When present in high concentrations, as in cholestatic liver diseases, bile acids can damage cells and cause inflammation. After the discovery of bile acids receptors about two decades ago, bile acids are considered signaling molecules. Besides regulating bile acid, xenobiotic, and nutrient metabolism, bile acids and their receptors have shown immunomodulatory properties and have been proposed as therapeutic targets for inflammatory diseases of the liver. This review focuses on bile acid-related signaling pathways that affect inflammation in the liver and provides an overview of the preclinical and clinical applications of modulators of these pathways for the treatment of cholestatic and autoimmune liver diseases.

Integrating the Synergy of the Gut Microbiome into Regenerative Medicine: Relevance to Neurological Disorders

A new paradigm of cell therapy-based approaches as a solution to several diseases caused by damage or loss of cells/tissues leading to organ failure heralded the birth of a new branch in medicine called regenerative medicine (RM), which was further fueled by in vitro cell expansion and tissue engineering (TE) technologies, including the ability to grow embryonic stem cells, induce pluripotent stem cells, and so on. RM addresses organ failure by repair, regeneration, or restoration, rejuvenation using cells, stem cells, or progenitor cells as tools having added cell-derived products also as a tool, and extracellular matrix component–based support, either direct or indirect (e.g., matrix induced autologous chondrocyte implantation) using scaffolds. Now, the main objective of RM is to solve the functional loss of cells that have evolved from cells as tools to cell-derived factors and scaffolds per se as tools. In this context, an important yet indispensable group of cells that constitute the major portion of the human body in terms of the number of cells having several essential roles to play, both directly and indirectly, starting from digestion and the immune system to the growing evidence of influencing neuronal function, aging, and carcinogenesis has been ignored. We would like to focus on these in this review as they should essentially be considered as a tool of RM, especially for neurological disorders for their vital role. What we are indicating is the second genome or the gut microbiome.

A new approach to testing mediation of the microbiome at both the community and individual taxon levels

MOTIVATION

Understanding whether and which microbes played a mediating role between an exposure and a disease outcome are essential for researchers to develop clinical interventions to treat the disease by modulating the microbes. Existing methods for mediation analysis of the microbiome are often limited to a global test of community-level mediation or selection of mediating microbes without control of the false discovery rate (FDR). Further, while the null hypothesis of no mediation at each microbe is a composite null that consists of three types of null, most existing methods treat the microbes as if they were all under the same type of null, leading to excessive false positive results.

RESULTS

We propose a new approach based on inverse regression that regresses the microbiome data at each taxon on the exposure and the exposure-adjusted outcome. Then, the P-values for testing the coefficients are used to test mediation at both the community and individual taxon levels. This approach fits nicely into our Linear Decomposition Model (LDM) framework, so our new method LDM-med, implemented in the LDM framework, enjoys all the features of the LDM, e.g. allowing an arbitrary number of taxa to be tested simultaneously, supporting continuous, discrete, or multivariate exposures and outcomes (including survival outcomes), and so on. Using extensive simulations, we showed that LDM-med always preserved the FDR of testing individual taxa and had adequate sensitivity; LDM-med always controlled the type I error of the global test and had compelling power over existing methods. The flexibility of LDM-med for a variety of mediation analyses is illustrated by an application to a murine microbiome dataset, which identified several plausible mediating taxa.

AVAILABILITY AND IMPLEMENTATION

Our new method has been added to our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Meta-Analysis of Caenorhabditis elegans Transcriptomics Implicates Hedgehog-Like Signaling in Host-Microbe Interactions

Controlling nematode-caused diseases that affect cattle and crops world-wide remains a critical economic issue, owing to the lack of effective sustainable interventions. The interdependence of roundworms and their environmental microbes, including their microbiota, offers an opportunity for developing more targeted anthelminthic strategies. However, paucity of information and a currently narrow understanding of nematode-microbe interactions limited to specific infection contexts has precluded us from exploiting it. With the advent of omics approaches to map host-microbe genetic interactions, particularly in the model roundworm Caenorhabditis elegans, large datasets are now available across multiple models, that enable identification of nematode-microbe-specific pathways. In this work we collected 20 transcriptomic datasets documenting gene expression changes of C. elegans exposed to 20 different commensal and pathogenic microbes, performing gene enrichment analyses followed by functional testing using RNA interference directed toward genes of interest, before contrasting results from transcriptomic meta-analyses and phenomics. Differential expression analyses revealed a broad enrichment in signaling, innate immune response and (lipid) metabolism genes. Amongst signaling gene families, the nematode-divergent and expanded Hedgehog-like signaling (HHLS) pathway featured prominently. Indeed, 24/60 C. elegans Hedgehog-like proteins (HRPs) and 15/27 Patched-related receptors (PTRs) were differentially expressed in at least four microbial contexts, while up to 32/60 HRPs could be differentially expressed in a single context. interestingly, differentially expressed genes followed a microbe-specific pattern, suggestive of an adaptive microbe-specific response. To investigate this further, we knocked-down 96 individual HHLS genes by RNAi, using high-throughput assays to assess their impact on three worm-gut infection models (Pseudomonas aeruginosa, Staphylococcus aureus, and Enterococcus faecalis) and two worm-commensal paradigms (Comamonas sp., and Bacillus subtilis). We notably identified new putative infection response genes whose upregulation was required for normal pathogen resistance (i.e., grl-21 and ptr-18 protective against E. faecalis), as well as commensal-specific host-gene expression changes that are required for normal host stress handling. Importantly, interactions appeared more microbe-specific than shared. Our results thus implicate the Hedgehog-like signaling pathway in the modulation and possibly fine-tuning of nematode-microbe interactions and support the idea that interventions targeting this pathway may provide a new avenue for anthelmintic development.

Microbiota in health and diseases

The role of microbiota in health and diseases is being highlighted by numerous studies since its discovery. Depending on the localized regions, microbiota can be classified into gut, oral, respiratory, and skin microbiota. The microbial communities are in symbiosis with the host, contributing to homeostasis and regulating immune function. However, microbiota dysbiosis can lead to dysregulation of bodily functions and diseases including cardiovascular diseases (CVDs), cancers, respiratory diseases, etc. In this review, we discuss the current knowledge of how microbiota links to host health or pathogenesis. We first summarize the research of microbiota in healthy conditions, including the gut-brain axis, colonization resistance and immune modulation. Then, we highlight the pathogenesis of microbiota dysbiosis in disease development and progression, primarily associated with dysregulation of community composition, modulation of host immune response, and induction of chronic inflammation. Finally, we introduce the clinical approaches that utilize microbiota for disease treatment, such as microbiota modulation and fecal microbial transplantation.

Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development

Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.

Lactobacillus paracasei CNCM I 1572: A Promising Candidate for Management of Colonic Diverticular Disease

Diverticular disease (DD) is a common gastrointestinal condition. Patients with DD experience a huge variety of chronic nonspecific symptoms, including abdominal pain, bloating, and altered bowel habits. They are also at risk of complications such as acute diverticulitis, abscess formation, hemorrhage, and perforation. Intestinal dysbiosis and chronic inflammation have recently been recognized as potential key factors contributing to disease progression. Probiotics, due to their ability to modify colonic microbiota balance and to their immunomodulatory effects, could present a promising treatment option for patients with DD. Lactobacillus paracasei CNCM I 1572 (LCDG) is a probiotic strain with the capacity to rebalance gut microbiota and to decrease intestinal inflammation. This review summarizes the available clinical data on the use of LCDG in subjects with colonic DD.

Compositional Quality and Possible Gastrointestinal Performance of Marketed Probiotic Supplements

The local pharmacies and shops are brimming with various probiotic products that herald a range of health benefits. The poor quality of probiotic products in both dosage and species is symptomatic of this multi-billion-dollar market making it difficult for consumers to single out reliable ones. This study aims to fill the potential gap in the labeling accuracy of probiotic products intended for human consumption. We describe a combinatorial approach using classical culture-dependent technique to quantify and molecular techniques (16 s rRNA gene sequencing, multilocus sequence, and ribotyping) for strain recognition of the microbial contents. The full gamut of probiotic characteristics including acid, bile and lysozyme tolerances, adhesiveness, anti-pathogenicity, and degree of safeness were performed. Their capacity to endure gastro-intestinal (GIT) stresses and select drugs was assessed in vitro. Our results forced us to declare that the local probiotic market is essentially unregulated. Almost none of the probiotic products tested met the label claim. Some (11%) have no viable cells, and a quarter (27%) showing significant inter-batch variation. A lower microbial count was typical with undesirables constituting a quarter of the total (~ 27%). Half of the products contained antibiotic-resistant strains; the unregulated use of these probiotics carries the risk of spreading antibiotic resistance to gut pathobionts. Poor tolerance to gut conditions and mediocre functionalism make the case worse. The current regulatory systems do not take this discrepancy into account. We recommend an evidence-based regular market surveillance of marketed probiotics to ensure the authenticity of the claims and product effectiveness.

The Gut Microbiome and Substance Use Disorder

Substance use disorders (SUDs) remain a significant public health challenge, affecting tens of millions of individuals worldwide each year. Often comorbid with other psychiatric disorders, SUD can be poly-drug and involve several different substances including cocaine, opiates, nicotine, and alcohol. SUD has a strong genetic component. Much of SUD research has focused on the neurologic and genetic facets of consumption behavior. There is now interest in the role of the gut microbiome in the pathogenesis of SUD. In this review, we summarize current animal and clinical evidence that the gut microbiome is involved in SUD, then address the underlying mechanisms by which the gut microbiome interacts with SUD through metabolomic, immune, neurological, and epigenetic mechanisms. Lastly, we discuss methods using various inbred and outbred mice models to gain an integrative understanding of the microbiome and host genetic controls in SUD.

Emerging Evidence of the Gut Microbiome in Chemotherapy: A Clinical Review

Increasing evidence suggests that the gut microbiome is associated with both cancer chemotherapy (CTX) outcomes and adverse events (AEs). This review examines the relationship between the gut microbiome and CTX as well as the impact of CTX on the gut microbiome. A literature search was conducted in electronic databases Medline, PubMed and ScienceDirect, with searches for "cancer" and "chemotherapy" and "microbiome/microbiota". The relevant literature was selected for use in this article. Seventeen studies were selected on participants with colorectal cancer (CRC; n=5), Acute Myeloid Leukemia (AML; n=3), Non-Hodgkin's lymphoma (n=2), breast cancer (BCa; n=1), lung cancer (n=1), ovarian cancer (n=1), liver cancer (n=1), and various other types of cancers (n=3). Seven studies assessed the relationship between the gut microbiome and CTX with faecal samples collected prior to (n=3) and following CTX (n=4) showing that the gut microbiome is associated with both CTX efficacy and toxicity. Ten other prospective studies assessed the impact of CTX during treatment and found that CTX modulates the gut microbiome of people with cancer and that dysbiosis induced by the CTX is related to AEs. CTX adversely impacts the gut microbiome, inducing dysbiosis and is associated with CTX outcomes and AEs. Current evidence provides insights into the gut microbiome for clinicians, cancer survivors and the general public. More research is required to better understand and modify the impact of CTX on the gut microbiome.

Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective

Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a multicultural society, but differences in gut microbiota persist across ethnicities. We hypothesized that migrant ethnic groups continue to share fundamental gut traits with the population in the country of origin due to shared cultural practices despite subsequent geographical separation. To test this hypothesis, the 16S rRNA gene amplicons from 16 studies comprising three major ethnic groups in Malaysia were analysed, covering 636 Chinese, 248 Indian and 123 Malay individuals from four countries (China, India, Indonesia and Malaysia). A confounder-adjusted permutational multivariate analysis of variance (PERMANOVA) detected a significant association between ethnicity and the gut microbiota (PERMANOVA R2=0.005, pseudo-F=2.643, P=0.001). A sparse partial least squares - discriminant analysis model trained using the gut microbiota of individuals from China, India and Indonesia (representation of Chinese, Indian and Malay ethnic group, respectively) showed a better-than-random performance in classifying Malaysian of Chinese descent, although the performance for Indian and Malay were modest (true prediction rate, Chinese=0.60, Indian=0.49, Malay=0.44). Separately, differential abundance analysis singled out Ligilactobacillus as being elevated in Indians. We postulate that despite the strong influence of geographical factors on the gut microbiota, cultural similarity due to a shared ethnic origin drives the presence of a shared gut microbiota composition. The interplay of these factors will likely depend on the circumstances of particular groups of migrants.

Intestinal Microbiota in Common Chronic Inflammatory Disorders Affecting Children

The incidence and prevalence rate of chronic inflammatory disorders is on the rise in the pediatric population. Recent research indicates the crucial role of interactions between the altered intestinal microbiome and the immune system in the pathogenesis of several chronic inflammatory disorders in children, such as inflammatory bowel disease (IBD) and autoimmune diseases, such as type 1 diabetes mellitus (T1DM) and celiac disease (CeD). Here, we review recent knowledge concerning the pathogenic mechanisms underlying these disorders, and summarize the facts suggesting that the initiation and progression of IBD, T1DM, and CeD can be partially attributed to disturbances in the patterns of composition and abundance of the gut microbiota. The standard available therapies for chronic inflammatory disorders in children largely aim to treat symptoms. Although constant efforts are being made to maximize the quality of life for children in the long-term, sustained improvements are still difficult to achieve. Additional challenges are the changing physiology associated with growth and development of children, a population that is particularly susceptible to medication-related adverse effects. In this review, we explore new promising therapeutic approaches aimed at modulation of either gut microbiota or the activity of the immune system to induce a long-lasting remission of chronic inflammatory disorders. Recent preclinical studies and clinical trials have evaluated new approaches, for instance the adoptive transfer of immune cells, with genetically engineered regulatory T cells expressing antigen-specific chimeric antigen receptors. These approaches have revolutionized cancer treatments and have the potential for the protection of high-risk children from developing autoimmune diseases and effective management of inflammatory disorders. The review also focuses on the findings of studies that indicate that the responses to a variety of immunotherapies can be enhanced by strategic manipulation of gut microbiota, thus emphasizing on the importance of proper interaction between the gut microbiota and immune system for sustained health benefits and improvement of the quality of life of pediatric patients.

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

BACKGROUND

Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples.

RESULTS

In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories.

CONCLUSIONS

The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.

Effect of arabinogalactan on the gut microbiome: A randomized, double-blind, placebo-controlled, crossover trial in healthy adults

OBJECTIVE

Promising evidence suggests beneficial health effects of arabinogalactan, but little is known about the effect of this non-digestible carbohydrate on the gut microbiota, a crucial mediator of human health. The objective of this study was to investigate the effect of an arabinogalactan product (ResistAid) on the fecal microbiome and short-chain fatty acids and gastrointestinal tolerance in healthy adults in a randomized, double-blind, crossover trial.

METHODS

Thirty adults were randomly assigned to consume 15 g/d maltodextrin (control) or ResistAid for 6 wk.

RESULTS

At week 6, compared to placebo, ResistAid supplementation led to a significant decrease in the ratio of fecal Firmicutes to Bacteroidetes, driven by an increase in Bacteroidetes and a decrease in Firmicutes. Moreover, the relative abundance of Bifidobacterium tended to increase with ResistAid supplementation. Additionally, ResistAid significantly decreased the α-diversity of the fecal microbiome. Predicted functional abundances based on 16S rRNA sequences showed that ResistAid supplementation increased the gene abundance of the gut microbiome for α-l-rhamnosidase, β-fructosidase, and levanase, as well as tricarboxylic acid and vitamin B₆ biosynthesis pathways. Fecal isovaleric, valeric, and hexanoic acids were significantly lower after ResistAid consumption. There were no statistically significant changes in bowel habit, stool consistency, gastrointestinal tolerance symptoms, chemistry profile, metabolic panel, or vitals, suggesting that consumption of 15 g daily ResistAid over 6 wk is safe.

CONCLUSION

These results demonstrate that the gut microbiome composition and predicted functions can be modulated by ResistAid consumption, perhaps suggesting a mechanistic explanation on its reported benefits in metabolic parameters and the immune system.

Probiotics as a Treatment for "Metabolic Depression"? A Rationale for Future Studies

Depression and metabolic diseases often coexist, having several features in common, e.g., chronic low-grade inflammation and intestinal dysbiosis. Different microbiota interventions have been proposed to be used as a treatment for these disorders. In the paper, we review the efficacy of probiotics in depressive disorders, obesity, metabolic syndrome and its liver equivalent based on the published experimental studies, clinical trials and meta-analyses. Probiotics seem to be effective in reducing depressive symptoms when administered in addition to antidepressants. Additionally, probiotics intake may ameliorate some of the clinical components of metabolic diseases. However, standardized methodology regarding probiotics use in clinical trials has not been established yet. In this narrative review, we discuss current knowledge on the recently used methodology with its strengths and limitations and propose criteria that may be implemented to create a new study of the effectiveness of probiotics in depressive disorders comorbid with metabolic abnormalities. We put across our choice on type of study population, probiotics genus, strains, dosages and formulations, intervention period, as well as primary and secondary outcome measures.

Microbiome-immune interactions in tuberculosis

Tuberculosis (TB) remains an infectious disease of global significance and a leading cause of death in low- and middle-income countries. Significant effort has been directed towards understanding Mycobacterium tuberculosis genomics, virulence, and pathophysiology within the framework of Koch postulates. More recently, the advent of “-omics” approaches has broadened our appreciation of how “commensal” microbes have coevolved with their host and have a central role in shaping health and susceptibility to disease. It is now clear that there is a diverse repertoire of interactions between the microbiota and host immune responses that can either sustain or disrupt homeostasis. In the context of the global efforts to combatting TB, such findings and knowledge have raised important questions: Does microbiome composition indicate or determine susceptibility or resistance to M. tuberculosis infection? Is the development of active disease or latent infection upon M. tuberculosis exposure influenced by the microbiome? Does microbiome composition influence TB therapy outcome and risk of reinfection with M. tuberculosis? Can the microbiome be actively managed to reduce risk of M. tuberculosis infection or recurrence of TB? Here, we explore these questions with a particular focus on microbiome-immune interactions that may affect TB susceptibility, manifestation and progression, the long-term implications of anti-TB therapy, as well as the potential of the host microbiome as target for clinical manipulation.

Mammalian Neuropeptides as Modulators of Microbial Infections: Their Dual Role in Defense versus Virulence and Pathogenesis

The regulation of infection and inflammation by a variety of host peptides may represent an evolutionary failsafe in terms of functional degeneracy and it emphasizes the significance of host defense in survival. Neuropeptides have been demonstrated to have similar antimicrobial activities to conventional antimicrobial peptides with broad-spectrum action against a variety of microorganisms. Neuropeptides display indirect anti-infective capacity via enhancement of the host’s innate and adaptive immune defense mechanisms. However, more recently concerns have been raised that some neuropeptides may have the potential to augment microbial virulence. In this review we discuss the dual role of neuropeptides, perceived as a double-edged sword, with antimicrobial activity against bacteria, fungi, and protozoa but also capable of enhancing virulence and pathogenicity. We review the different ways by which neuropeptides modulate crucial stages of microbial pathogenesis such as adhesion, biofilm formation, invasion, intracellular lifestyle, dissemination, etc., including their anti-infective properties but also detrimental effects. Finally, we provide an overview of the efficacy and therapeutic potential of neuropeptides in murine models of infectious diseases and outline the intrinsic host factors as well as factors related to pathogen adaptation that may influence efficacy.

Adiposity in Depression or Depression in Adiposity? The Role of Immune-Inflammatory-Microbial Overlap

Some of the most common and debilitating conditions are metabolic disorders (metabolic syndrome and non-alcoholic fatty liver disease) and depression. These conditions are also exacerbated by the fact that they often co-occur. Although the exact mechanisms underlying such relationships are poorly known, antipsychotic medication and antidepressant use, diet and physical activity, and lifestyle factors are believed to play a role; however, their high co-occurrence rate suggests a possible pathophysiological overlap. This paper reviews several possible bases for this overlap, including hypothalamic-pituitary-adrenal axis dysregulation, immune alterations with chronic inflammation, and oxidative stress. While it is entirely possible that changes in the microbiota may play a role in each of them, interventions based on the implementation of dietary and other lifestyle changes, supplementation with prebiotics or probiotics and faecal microbiota transplantation have failed to achieve conclusive results. A better characterization of the above associations may allow a more targeted approach to the treatment of both depressive and metabolic disorders. The paper also presents several practical applications for future studies.

Probiotics and MicroRNA: Their Roles in the Host-Microbe Interactions

Probiotics are widely accepted to be beneficial for the maintenance of the gut homeostasis - the dynamic and healthy interactions between host and gut microorganisms. In addition, emerging as a key molecule of inter-domain communication, microRNAs (miRNAs) can also mediate the host-microbe interactions. However, a comprehensive description and summary of the association between miRNAs and probiotics have not been reported yet. In this review, we have discussed the roles of probiotics and miRNAs in host-microbe interactions and proposed the association of probiotics with altered miRNAs in various intestinal diseases and potential molecular mechanisms underlying the action of probiotics. Furthermore, we provided a perspective of probiotics-miRNA-host/gut microbiota axis applied in search of disease management highly associated with the gut microbiome, which will potentially prove to be beneficial for future studies.

Microbiome: Emerging Concepts in Patients with Chronic Liver Disease

The gut microbiome is an exciting new area of research in chronic liver disease. It has shown promise in expanding our understanding of these complicated disease processes and has opened up new treatment modalities. The aim of this review is to increase understanding of the microbiome and explain the collection and analysis process in the context of liver disease. It also looks at our current understanding of the role of the microbiome in the wide spectrum of chronic liver diseases and how it is being used in current therapies and treatments.

Selection of Wild Lactic Acid Bacteria Strains as Promoters of Postbiotics in Gluten-Free Sourdoughs

The occurrence of inflammatory responses in humans is frequently associated with food intolerances and is likely to give rise to irritable bowel disease. The use of conventional or unconventional flours to produce gluten-free baking doughs brings important technological and nutritional challenges, and the use of the sourdough biotechnology has the potential to overcome such limitations. In addition, the typical metabolic transformations carried out by Lactic Acid Bacteria (LAB) can become an important biotechnological process for the nutritional fortification and functionalization of sourdoughs due to the resulting postbiotics. In such a context, this research work aimed at isolating and selecting new LAB strains that resort to a wide range of natural environments and food matrices to be ultimately employed as starter cultures in gluten-free sourdough fermentations. Nineteen LAB strains belonging to the genera of Lactobacillus, Leuconostoc, Pediococcus, and Streptococcus were isolated, and the selection criteria encompassed their acidification capacity in fermentations carried out on chickpea, quinoa, and buckwheat flour extracts; the capacity to produce exopolysaccharides (EPS); and the antimicrobial activity against food spoilage molds and bacteria. Moreover, the stability of the LAB metabolites after the fermentation of the gluten-free flour extracts submitted to thermal and acidic treatments was also assessed.