Repertoire of human gut microbes

The communication mechanism of the gut-brain axis and its effect on central nervous system diseases: A systematic review

Gut microbiota is involved in intricate and active metabolic processes the host's brain function, especially its role in immune responses, secondary metabolism, and symbiotic connections with the host. Gut microbiota can promote the production of essential metabolites, neurotransmitters, and other neuroactive chemicals that affect the development and treatment of central nervous system diseases. This article introduces the relevant pathways and manners of the communication between the brain and gut, summarizes a comprehensive overview of the current research status of key gut microbiota metabolites that affect the functions of the nervous system, revealing those adverse factors that affect typical communication between the brain-gut axis, and outlining the efforts made by researchers to alleviate these neurological diseases through targeted microbial interventions. The relevant pathways and manners of communication between the brain and gut contribute to the experimental design of new treatment plans and drug development. The factors that may cause changes in gut microbiota and affect metabolites, as well as current intervention methods are summarized, which helps improve gut microbiota brain dialogue, prevent adverse triggering factors from interfering with the gut microbiota system, and minimize neuropathological changes.

Metagenomic discovery of microbial eukaryotes in stool microbiomes

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.

A catalog of ethanol-producing microbes in humans

Aim: Endogenous ethanol production emerges as a mechanism of nonalcoholic steatohepatitis, obesity, diabetes and auto-brewery syndrome. Methods: To identify ethanol-producing microbes in humans, we used the NCBI taxonomy browser and the PubMed database with an automatic query and manual verification. Results: 85 ethanol-producing microbes in human were identified. Saccharomyces cerevisiae, Candida and Pichia were the most represented fungi. Enterobacteriaceae was the most represented bacterial family with mainly Escherichia coli and Klebsiella pneumoniae. Species of the Lachnospiraceae and Clostridiaceae family, of the Lactobacillales order and of the Bifidobacterium genus were also identified. Conclusion: This catalog will help the study of ethanol-producing microbes in human in the pathophysiology, diagnosis, prevention and management of human diseases associated with endogenous ethanol production.

Metabolic Syndrome: A Narrative Review from the Oxidative Stress to the Management of Related Diseases

Metabolic syndrome (MS) is a growing disorder affecting thousands of people worldwide, especially in industrialised countries, increasing mortality. Oxidative stress, hyperglycaemia, insulin resistance, inflammation, dysbiosis, abdominal obesity, atherogenic dyslipidaemia and hypertension are important factors linked to MS clusters of different pathologies, such as diabesity, cardiovascular diseases and neurological disorders. All biochemical changes observed in MS, such as dysregulation in the glucose and lipid metabolism, immune response, endothelial cell function and intestinal microbiota, promote pathological bridges between metabolic syndrome, diabesity and cardiovascular and neurodegenerative disorders. This review aims to summarise metabolic syndrome's involvement in diabesity and highlight the link between MS and cardiovascular and neurological diseases. A better understanding of MS could promote a novel strategic approach to reduce MS comorbidities.

Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study

Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.

Harnessing the power of probiotics to enhance neuroplasticity for neurodevelopment and cognitive function in stunting: a comprehensive review

BACKGROUND

Stunting become a global concern because it's not only affecting physical stature, but also affecting on neurodevelopment and cognitive function. These impacts are resulting in long-term consequences especially for human resources, such as poor-quality labor, decreased productivity due to decreasing of health quality, including immunity and cognitive aspect.

DISCUSSION

This comprehensive review found that based on many studies, there is an altered gut microbiota, or dysbiosis, in stunted children, causing the impairment of brain development through Microbiota-Gut Brain Axis (MGB Axis) mechanism. The administration of probiotics has been known affect MGBA by improving the physical and chemical gut barrier integrity, producing antimicrobial substance to inhibit pathogen, and recovering the healthy gut microbiota. Probiotics, along with healthy gut microbiota, produce SCFAs which have various positive impact on CNS, such as increase neurogenesis, support the development and function of microglia, reduce inflammatory signaling, improve the Blood Brain Barrier's (BBB's) integrity, produce neurotropic factors (e.g. BDNF, GDNF), and promote the formation of new synapse. Probiotics also could induce the production of IGF-1 by intestinal epithelial cells, which functioned as growth factor of multiple body tissues and resulted in improvement of linear growth as well as brain development.

CONCLUSION

These properties of probiotics made it become the promising and feasible new treatment approach for stunting. But since most of the studies in this field are conducted in animal models, it is necessary to translate animal data into human models and do additional study to identify the numerous components in the MGB axis and the effect of probiotics on human.

Berberine-induced glucagon-like peptide-1 and its mechanism for controlling type 2 diabetes mellitus: a comprehensive pathway review

Introduction: A growing number of studies have thus far showed the association between type 2 diabetes mellitus (DM) and the intestinal microbiome homoeostasis. As reported, the gut microflora can be significantly different in patients with type 2 DM (T2DM) compared to those in healthy individuals.Methods: The authors collected the relevant articles published until 2022 and these are carefully selected from three scientific databases based on keywords.Discussion: This review highlights research on the anti-diabetic properties of berberine (BBR)-induced glucagon-like peptide-1 (GLP-1), as a glucose-lowering factor and a balance regulator in the microbial flora of the intestines, which plays an important role in adjusting the signalling pathways affecting insulin secretion.Results: Considering the anti-diabetic characteristics of the BBR-induced GLP-1, BBR makes a promising complementary treatment for reducing the clinical symptoms of DM by reducing the hyperglycaemia. Berberin might be a safe and effective drug for T2DM with little or no adverse effects.HighlightsBerberine induces GLP-1 insulin secretion by PLC2 pathway in the intestinalBerberine-induced GLP-1 decreases mitochondrial stress and relocates cytochrome c out of the mitochondria.Berberine induces GLP-1 secretion in the intestine by altering the bacterial profile, thus could possibly lighten diabetes symptomsBerberine-induced SCFA production, SCFA causes GLP-1 secretion from the intestinal L-Cell.Preventing mitochondrial damage, reducing adipose tissue fat, and reducing oxidative stress are thus among the results of BBR-induced GLP-1.The lower costs of BBR, and its limited side effects and higher availability, make it a promising supplementary medicine for DM.

The clinical value of anal swabs for microbial detection in allogeneic haematopoietic stem cell transplantation

The intestinal microbiota plays critical roles in allogeneic hematopoietic stem cell transplantation (allo-HSCT). Rapid and effective microbial detection methods have important guiding value for the selection of intervention strategies for allo-HSCT recipients. We evaluated the application of the anal swab test before transplantation in allo-HSCT recipients. A total of 120 patients who underwent anal swab testing before allo-HSCT were retrospectively analyzed and divided into 3 groups: sterile (aseptic growth-negative), G+ (gram-positive bacterial colonization), and G- (gram-negative bacterial colonization). On 16S rRNA sequencing, gram-negative bacteria predominated in the G- group before and after transplantation. Compared with the sterile group, the percentage of natural killer cells was higher and the percentage of T cells was lower after transplantation in the G- group at 1 month after transplantation. The percentage of CD4+ and CD4+CD8+ T cells was lower and the percentage of regulatory T cells was higher in the G- group. The plasma levels of proinflammatory cytokines (TNF-α, IFN-γ, IL-6, and IL-17A) at 2 weeks post-transplantation were lower in the G- group than in the sterile group, as was the cumulative incidence of grade III-IV acute graft-versus-host disease (GVHD). Gram-negative bacterial colonization before allo-HSCT was associated with low rates of bloodstream infections within 100 days post-transplantation and cytomegalovirus reactivation at 100 days to 2 years post-transplantation. Moreover, patients in the G- group had a higher rate of 2-year GVHD-free, relapse-free survival compared with patients in the sterile group. The detection results using anal swabs were consistent with the gram-negative or gram-positive bacteria abundance of 16S rRNA sequencing results and associated with immune homeostasis and clinical outcomes after allo-HSCT. Anal swab testing may have potential advantages as a simple and effective method for microbial detection in allo-HSCT.

Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives

Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.

The human gut virome: composition, colonization, interactions, and impacts on human health

The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.

Environmental factors and gut microbiota: Toward better conservation of deer species

Thousands of microbial species inhabiting the animal gut, collectively known as the gut microbiota, play many specific roles related to host nutrient metabolism and absorption, immune regulation, and protection from pathogenic bacteria. Gut microbiota composition is affected by several internal and external factors, such as the host genotype, dietary intake, breeding environment, and antibiotic exposure. As deer species are important members for maintaining ecosystem balance, understanding the effects of multiple factors on the gut microbiota of deer species, particularly endangered ones, is crucial. In this review, we summarize and discuss the factors that significantly affect the gut microbiota of deer and present the impacts of these factors on microbial composition. In particular, we focused on the changes in gut microbiota due to dietary differences under different conditions, including seasonal changes, different geographical locations, and captivity, as well as weaning and pathogen disturbance. Understanding the correlations between gut microbiota composition and its driving factors is important for evaluating and improving the captive breeding environment for better conservation of endangered deer species, and reintroducing wild deer populations in the future.

The ameliorative effect of probiotics on diet-induced lipid metabolism disorders: A review

High-fat diet induces lipid metabolism disorders that has become one of the grievous public health problems and imposes a serious economic and social burden worldwide. Safety probiotics isolated from nature are regarded as a novel supplementary strategy for preventing and improving diet-induced lipid metabolism disorders and related chronic diseases. The present review summarized the latest researches of probiotics in high fat diet induced lipid metabolism disorders to provide a critical perspective on the regulatory function of probiotics for future research. Furthermore, the screening criteria and general sources of probiotics with lipid-lowering ability also outlined to enlarge microbial species resource bank instantly, which promoted the development of functional foods with lipid-lowering strains from nature. After critically reviewing the lipid-lowering potential of probiotics both in vitro and in vivo and even in clinical data of humans, we provided a perspective that probiotics activated AMPK signaling pathway to regulate fat synthesis and decomposition, as well as affected positively the gut microbiota structure, intestinal barrier function and systemic inflammatory response, then these beneficial effects are amplified along Gut-liver axis, which regulated intestinal flora metabolites such as SCFAs and BAs by HMGCR/FXR/SHP signaling pathway to improve high fat diet induced lipid metabolism disorders effectively.

Changes in Gut Microbiota Composition Associated with the Presence of Enteric Protist Blastocystis in Captive Forest Musk Deer (Moschus Berezovskii)

Blastocystis is a common protistan parasite inhabiting the gastrointestinal tract of a wide range of hosts including humans and domestic and wild animals. Many studies have revealed the associations between Blastocystis and gut microbiome in humans. However, only a few studies have focused on the associations between Blastocystis and gut microbiome of animals, especially in forest musk deer (Moschus berezovskii). We investigated the effects of the Blastocystis colonization on the intestinal bacterial community compositions using amplicon sequencing targeting the V4 variable region of the 16S rRNA. Two subtypes of Blastocystis (ST5 and ST10) and Blastocystis-free (control) were included in this study. We found that compared with the forest musk deer without Blastocystis, ST10-colonized forest musk deer had higher bacterial richness and diversity, while ST5-colonized forest musk deer showed a comparable bacterial diversity. Likewise, beta diversity revealed significant differences in bacterial community structure between ST10-colonized and Blastocystis-free forest musk deer. The proportion of Bacteroidetes were significantly enriched in ST10-colonized forest musk deer. Bacterial community structure between ST5-colonized and Blastocystis-free forest musk deer did not differ significantly. The present study explored the associations between Blastocystis and gut microbial community of forest musk deer for the first time, and revealed ST10 colonization, instead of ST5, is associated with higher bacterial diversity and shifted microbial structure. Our data provides valuable insights into the associations between gut microbiomes and parasites.

IMPORTANCE Forest musk deer is listed as an endangered species by International Union for Conservation of Nature Red List, and the Chinese government has introduced captivity breeding measures to curb the rapid decline of the musk deer population since the 1950s. It has been suggested that Blastocystis colonization can modulate the composition of the host's intestinal microbiota, thereby affecting the host health. The present study investigated the effects of the Blastocystis colonization on the gut microbiota in the feces of forest musk deer in Sichuan Province, China. Two subtypes (ST5 and ST10) have differential effects on the bacterial diversity and community composition, suggesting that the study of Blastocystis should be distinguished at the subtype level. Because the pathogenicity of Blastocystis is controversial, pathogenic, or commensal, continuous monitoring of the impact of Blastocystis colonization on the intestinal microbiota is of great significance to assess its health effects on forest musk deer.

The final fate of food: On the establishment of in vitro colon models

The search for life/health quality has driven the search for a better understanding of food components on the overall individual health, which turns to be intrinsically related to the digestive system. In vitro digestion models are considered an alternative for the in vivo studies for a variety of practical reasons, but further research is still needed concerning the colon model establishment. An effective in vitro colon model should consider all unit operations and transport phenomena, together with chemical and biochemical reactions, material handling and reactor design. Due to the different techniques and dependence on the donor microbiota, it is difficult to obtain a standard protocol with results reproductible in time and space. Furthermore, the colon model should be fed with a representative substrate, thus what happens in upper digestion tract and absorption prior to colon is also of crucial importance. Essentially, there are two ways to think about how to achieve a good and useful in vitro colon model: a complex biomimetic system that provides results comparable with the in vivo studies or a simple system, that despite the fact it could not give physiologically relevant data, it is sufficient to understand the fate of some specific components.

Gut Microbiota: A Potential Target for Cancer Interventions

The gut microbiota plays a crucial role in many physiological processes in the human body. Dysbiosis can disrupt the intestinal barrier and alter metabolism and immune responses, leading to the development of diseases. Over the past few decades, evidence has accumulated linking changes in the composition of the gut microbiota to dozens of seemingly unrelated conditions, including cancer. Overall, the gut microbiota mainly affects the occurrence and development of cancer by damaging host DNA, forming and maintaining a pro-inflammatory environment, and affecting host immune responses. In addition, the gut microbiota can also affect the efficacy and toxicity of chemotherapy, radiotherapy, and immunotherapy. Scientists attempt to improve the efficacy and decrease the toxicity of these treatment modalities by fine-tuning the gut microbiota. The aim of this review is to assist researchers and clinicians in developing new strategies for the detection and treatment of tumors by providing the latest information on the intestinal microbiome and cancer, as well as exploring potential application prospects and mechanisms of action.

Gut Microbiota and Neuroplasticity

The accumulating evidence linking bacteria in the gut and neurons in the brain (the microbiota-gut-brain axis) has led to a paradigm shift in the neurosciences. Understanding the neurobiological mechanisms supporting the relevance of actions mediated by the gut microbiota for brain physiology and neuronal functioning is a key research area. In this review, we discuss the literature showing how the microbiota is emerging as a key regulator of the brain's function and behavior, as increasing amounts of evidence on the importance of the bidirectional communication between the intestinal bacteria and the brain have accumulated. Based on recent discoveries, we suggest that the interaction between diet and the gut microbiota, which might ultimately affect the brain, represents an unprecedented stimulus for conducting new research that links food and mood. We also review the limited work in the clinical arena to date, and we propose novel approaches for deciphering the gut microbiota-brain axis and, eventually, for manipulating this relationship to boost mental wellness.

β-Elemene Suppresses Obesity-Induced Imbalance in the Microbiota-Gut-Brain Axis

As a kind of metabolically triggered inflammation, obesity influences the interplay between the central nervous system and the enteral environment. The present study showed that β-elemene, which is contained in various plant substances, had effects on recovering the changes in metabolites occurring in high-fat diet (HFD)-induced obese C57BL/6 male mice brains, especially in the prefrontal cortex (PFC) and hippocampus (HIP). β-elemene also partially reversed HFD-induced changes in the composition and contents of mouse gut bacteria. Furthermore, we evaluated the interaction between cerebral metabolites and intestinal microbiota via Pearson correlations. The prediction results suggested that Firmicutes were possibly controlled by neuron integrity, cerebral inflammation, and neurotransmitters, and Bacteroidetes in mouse intestines might be related to cerebral aerobic respiration and the glucose cycle. Such results also implied that Actinobacteria probably affected cerebral energy metabolism. These findings suggested that β-elemene has regulatory effects on the imbalanced microbiota-gut-brain axis caused by obesity and, therefore, would contribute to the future study in on the interplay between cerebral metabolites from different brain regions and the intestinal microbiota of mice.

Leukaemia Infection Diagnosis and Intestinal Flora Disorder

Leukaemia is the most common malignant tumor in childhood and can be cured by chemotherapy. Infection is an important cause of treatment-related death and treatment failure in childhood leukaemia. Recent studies have shown that the correlation between the occurrence of leukaemia infection and the intestinal flora has attracted more and more attention. Intestinal flora can affect the body's physiological defense and immune function. When intestinal microflora disorder occurs, metabolites/microorganisms related to intestinal flora alterations and even likely the associated morpho-functional alteration of the epithelial barrier may be promising diagnostic biomarkers for the early diagnosis of leukaemia infection. This review will focus on the interaction between leukaemia infection and intestinal flora, and the influence of intestinal flora in the occurrence and development of leukaemia infection.

An Oral FMT Capsule as Efficient as an Enema for Microbiota Reconstruction Following Disruption by Antibiotics, as Assessed in an In Vitro Human Gut Model

Fecal microbiota transplantation (FMT) is an innovative therapy already used in humans to treat Clostridioides difficile infections associated with massive use of antibiotics. Clinical studies are obviously the gold standard to evaluate FMT efficiency but remain limited by regulatory, ethics, and cost constraints. In the present study, an in vitro model of the human colon reproducing medically relevant perturbation of the colonic ecosystem by antibiotherapy was used to compare the efficiency of traditional FMT enema formulations and a new oral capsule in restoring gut microbiota composition and activity. Loss of microbial diversity, shift in bacterial populations, and sharp decrease in fermentation activities induced in vivo by antibiotherapy were efficiently reproduced in the in vitro model, while capturing inter-individual variability of gut microbiome. Oral capsule was as efficient as enema to decrease the number of disturbed days and bacterial load had no effect on enema performance. This study shows the relevance of human colon models as an alternative approach to in vivo assays during preclinical studies for evaluating FMT efficiency. The potential of this in vitro approach could be extended to FMT testing in the management of many digestive or extra-intestinal pathologies where gut microbial dysbiosis has been evidenced such as inflammatory bowel diseases, obesity or cancers.

Human gut microbiota and its association with pathogenesis and treatments of neurodegenerative diseases

Human gut microbiota consists of various microorganisms whose numbers are similar to those of human cells. Human gut microbes and the brain form bidirectional communications through the brain-gut-axis, and play a central role in normal physiological processes and in pathogenesis of many human diseases. Accumulating evidence has demonstrated the crucial effect of gut microbes in proper brain functions and under disease conditions. Here we first focus on revealing current knowledge of the role of gut microbes in neural development and functions. We then summarize mutual relationships between gut microbes and human diseases, in particular neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease and Multiple sclerosis. Finally, we highlight ongoing studies in exploring gut microbes in treatments of human diseases. Applying gut microbes as a means in treatment of human diseases is becoming a promising research direction, and has a great potential in clinical practice.

Updating the repertoire of cultured bacteria from the human being

The recent renewal of cultural approach has substantially enriched knowledge of the human microbiota, notably through the discovery of new taxa from various anatomical sites. As an increasing number of these recent species are currently considered beneficial or harmful for human health, a constant updating of the repertoire of bacteria and archaea isolated from humans by culture is essential. Herein, we show that the number of cultured bacterial species associated with human beings increased, from 2776 in 2018, to 3253 in 2020, representing a 17% increase in 2 years by adding 477 species, of which 64% are new species (N = 307). A wide majority of the species added (i.e., 63%) were isolated using the culturomics approach, while 16% were cultured as part of clinical microbiology laboratories. Human microbiota studies would benefit from the completeness of the repertoire of bacteria associated with human beings, which would require continued efforts to culture microbes from human specimens.

An effective culturomics approach to study the gut microbiota of mammals

The microbial characterization of the mammal's gut is an emerging research area, wherein culturomics methodologies applied to human samples are transposed to the animal context without improvement. In this work, using Egyptian mongoose as a model, we explore wet bench conditions to define an effective experimental design based on culturomics and DNA barcoding with potential application to different mammal species. After testing a battery of solid media and enrichments, we show that YCFA-based media, in aerobic and anaerobic conditions, together with PDA supplemented with chloramphenicol, are sufficient to maximize bacterial and fungal microbiota diversity. The pasteurization of the sample enrichment before cultivation is central to gain insight into sporogenic communities. We suggest the application of this optimized culturomics strategy to accurately expand knowledge on the microbial richness of mammals' gut, maximizing the application of common laboratory resources, without dramatic time and consumables expenditure but with high resolution of microbial landscapes. The analysis of ten fecal samples proved adequate to assess the core gastrointestinal microbiota of the mesocarnivore under analysis. This approach may empower most microbiology laboratories, particularly the veterinary, to perform studies on mammal's microbiota, and, in contrast with metagenomics, enabling the recovery of live bacteria for further studies.

A Significant Question in Cancer Risk and Therapy: Are Antibiotics Positive or Negative Effectors? Current Answers and Possible Alternatives

Cancer is predominantly considered as an environmental disease caused by genetic or epigenetic alterations induced by exposure to extrinsic (e.g., carcinogens, pollutants, radiation) or intrinsic (e.g., metabolic, immune or genetic deficiencies). Over-exposure to antibiotics, which is favored by unregulated access as well as inappropriate prescriptions by physicians, is known to have led to serious health problems such as the rise of antibiotic resistance, in particular in poorly developed countries. In this review, the attention is focused on evaluating the effects of antibiotic exposure on cancer risk and on the outcome of cancer therapeutic protocols, either directly acting as extrinsic promoters, or indirectly, through interactions with the human gut microbiota. The preponderant evidence derived from information reported over the last 10 years confirms that antibiotic exposure tends to increase cancer risk and, unfortunately, that it reduces the efficacy of various forms of cancer therapy (e.g., chemo-, radio-, and immunotherapy alone or in combination). Alternatives to the current patterns of antibiotic use, such as introducing new antibiotics, bacteriophages or enzybiotics, and implementing dysbiosis-reducing microbiota modulatory strategies in oncology, are discussed. The information is in the end considered from the perspective of the most recent findings on the tumor-specific and intracellular location of the tumor microbiota, and of the most recent theories proposed to explain cancer etiology on the notion of regression of the eukaryotic cells and systems to stages characterized for a lack of coordination among their components of prokaryotic origin, which is promoted by injuries caused by environmental insults.

Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa

To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3–V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.

The Gene Catalog and Comparative Analysis of Gut Microbiome of Big Cats Provide New Insights on Panthera Species

Majority of metagenomic studies in the last decade have focused on revealing the gut microbiomes of humans, rodents, and ruminants; however, the gut microbiome and genic information (gene catalog) of large felids such as Panthera species are largely unknown to date. In this study, the gut bacterial, fungal, and viral metagenomic composition was assessed from three Panthera species (lion, leopard, and tiger) of Indian origin, which were consuming the same diet and belonged to the same geographical location. A non-redundant bacterial gene catalog of the Panthera gut consisting of 1,507,035 putative genes was constructed from 27 Panthera individuals, which revealed a higher abundance of purine metabolism genes correlating with their purine-rich dietary intake. Analysis with Carbohydrate Active enZyme (CAZy) and MEROPS databases identified enrichment of glycoside hydrolases (GHs), glycoside-transferases, and collagenases in the gut, which are important for nutrient acquisition from animal biomass. The bacterial, fungal, and viral community analysis provided the first comprehensive insights into the Panthera-specific microbial community. The Panthera gene catalog and the largest comparative study of the gut bacterial composition of 68 individuals of Carnivora species from different geographical locations and diet underscore the role of diet and geography in shaping the Panthera gut microbiome, which is significant for the health and conservation management of these highly endangered species.

Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome

Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (Herpestes ichneumon) gut microbiota across sex and age classes by microbial profiling. In this study, we generate, through culturomics, extended baseline information on the culturable bacterial and fungal microbiome of the species using the same specimens as models. Firstly, this strategy enabled us to explore cultivable microbial community differences across sexes and to ascertain the influence exerted by biological and environmental contexts of each host in its microbiota signature. Secondly, it permitted us to compare the culturomics and microbial profiling approaches and their ability to provide information on mongoose gut microbiota. In agreement with microbial profiling, culturomics showed that the core gut cultivable microbiota of the mongoose is dominated by Firmicutes and, as previously found, is able to distinguish sex- and age class-specific genera. Additional information could be obtained by culturomics, with six new genera unveiled. Richness indices and the Shannon index were concordant between culture-dependent and culture-independent approaches, highlighting significantly higher values when using microbial profiling. However, the Simpson index underlined higher values for the culturomics-generated data. These contrasting results were due to a differential influence of dominant and rare taxa on those indices. Beta diversity analyses of culturable microbiota showed similarities between adults and juveniles, but not in the data series originated from microbial profiling. Additionally, whereas the microbial profiling indicated that there were several bioenvironmental features related to the bacterial gut microbiota of the Egyptian mongoose, a clear association between microbiota and bioenvironmental features could not be established through culturomics. The discrepancies found between the data generated by the two methodologies and the underlying inferences, both in terms of β-diversity and role of bioenvironmental features, confirm that culture-independent, sequence-based methods have a higher ability to assess, at a fine scale, the influence of abiotic and biotic factors on the microbial community composition of mongoose' gut. However, when used in a complementary perspective, this knowledge can be expanded by culturomics.

Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities

The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the "microscomics" approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our culture-independent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect "minimicrobes" Candidate Phyla Radiation (CPR) for the first time in human stool samples. This "microscomics" approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.

Egyptian Mongoose (Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes

The Egyptian mongoose (Herpestes ichneumon) is a medium-size carnivore that, in Europe, is restricted to Iberia. The bio-ecology of this species remains to be elucidated in several dimensions, including gut microbiota that is nowadays recognized as a fundamental component of mammals. In this work, we investigated the gut microbiota of this herpestid by single-molecule real-time sequencing of twenty paired male (n = 10) and female (n = 10) intestinal samples. This culture-independent approach enabled microbial profiling based on 16S rDNA and investigation of taxonomical and functional features. The core gut microbiome of the adult subpopulation was dominated by Firmicutes, Fusobacteria, Actinobacteria, and Proteobacteria. Eight genera were uniquely found in adults and five in non-adults. When comparing gut bacterial communities across sex, four genera were exclusive of females and six uniquely found in males. Despite these compositional distinctions, alpha- and beta-diversity analyses showed no statistically significant differences across sex or between adult and non-adult specimens. However, when function was inferred, males presented a significantly higher abundance of amino acid and citrate cycle metabolic pathways, compared to the significant overrepresentation in females of galactose metabolic pathways. Additionally, adults exhibited a significantly higher abundance of cationic antimicrobial peptide resistance pathways, while non-adults bared a significant overrepresentation of two-component systems associated with antibiotic synthesis, flagellin and biofilm production, and chemotaxis control. This study adds new insights into the mongoose bio-ecology palette, highlighting taxonomical and functional microbiome dissimilarities across sex and age classes, possibly related to primary production resources and life-history traits that impact on behavior and diet.

The impact of probiotics, prebiotics, and synbiotics on the biochemical, clinical, and immunological markers, as well as on the gut microbiota of obese hosts

Obesity is currently considered a global epidemic and it leads to several alterations on the human body and its metabolism. There are evidences showing that the intestinal microbiota can influence on the pathogenesis of obesity. Microbiota plays a vital role not only in the digestion and absorption of nutrients, but also in the homeostatic maintenance of host immunity, metabolism, and gut barrier. Its dietary alteration is an important target in the treatment of obesity. Emerging evidence suggests that modifying the composition of the gut microbiota through probiotic, prebiotic, and synbiotic supplementation may be a viable adjuvant treatment option for obese individuals. In this review, the impact of probiotics, prebiotics, and synbiotics on the anthropometric profile, biochemical regulation, clinical, and immunological markers, as well as on the gut microbiota of obese hosts is described. It also emphasizes how changes in the composition and/or metabolic activity of the gut microbiota through the administration of nutrients with probiotic, prebiotic, or synbiotic properties can modulate the host's gene expression and metabolism, and thereby positively influence on the host's adipose tissue development and related metabolic disorders. The beneficial effects on the host's metabolism promoted by prebiotics, probiotics, and synbiotics have been successfully demonstrated by several studies. However, further investigation is needed to fully explain the cellular mechanisms of action of probiotics and prebiotics on human health, and also to elucidate the relationship between microbiota and obesity etiology, using well-designed, long-term, and large-scale clinical interventions.

The Relationship between Prevention and Treatment of Colorectal Cancer and Cancerous Toxin Pathogenesis Theory Basing on Gut Microbiota

Gut microbiota is a diverse consortium of bacteria, fungi, protozoa, and viruses in the gut of all mammals. Gut microbiota remains in steady state under normal conditions. Changes in the internal and external environment may cause gut Microbiota to be out of tune. Malignant tumors are one of the major diseases currently endangering human health. CRC (colorectal cancer) has a significant upward trend in morbidity and mortality in many parts of the world. Technological advances have not yet brought about a breakthrough in the efficacy of CRC. The development of colon cancer is closely related to gut microbiota imbalance. According to more than 60 years of clinical practice, Professor Zhongying Zhou first proposed the pathogenesis theory of "cancerous toxin" in the 1990s and believed that cancerous toxin was a key pathogenesis of tumor development. Under the guidance of the theory of cancerous toxin, combined with clinical practice, Professor Zhou created an effective anticancer Chinese herbal compound, Jiedu Xiaoai Prescription. This paper summarizes recent hotspots related to gut microbiota and the occurrence, development, and prevention of colon cancer at home and abroad. The relationship between gut microbiota and cancerous toxin theory is proposed, and the feasibility of further studying the biological basis of cancerous toxin pathogenesis theory from the perspective of gut microbiota is pointed out.

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences

A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota

OBJECTIVE

Human gut microbiome studies are mainly bacteria- and archaea-oriented, overlooking the presence of single-cell eukaryotes such as Blastocystis, an enteric stramenopiles with worldwide distribution. Here, we surveyed the prevalence and subtype variation of Blastocystis in faecal samples collected as part of the Flemish Gut Flora Project (FGFP), a Western population cohort. We assessed potential links between Blastocystis subtypes and identified microbiota-host covariates and quantified microbiota differentiation relative to subtype abundances.

DESIGN

We profiled stool samples from 616 healthy individuals from the FGFP cohort as well as 107 patients with IBD using amplicon sequencing targeting the V4 variable region of the 16S rRNA and 18S rRNA genes. We evaluated associations of Blastocystis, and their subtypes, with host parameters, diversity and composition of bacterial and archaeal communities.

RESULTS

Blastocystis prevalence in the non-clinical population cohort was 30% compared with 4% among Flemish patients with IBD. Within the FGFP cohort, out of 69 previously identified gut microbiota covariates, only age was associated with Blastocystis subtype carrier status. In contrast, a strong association between microbiota community composition and Blastocystis subtypes was observed, with effect sizes larger than that of host covariates. Microbial richness and diversity were linked to both Blastocystis prevalence and subtype variation. All Blastocystis subtypes detected in this cohort were found to be less prevalent in Bacteroides enterotyped samples. Interestingly, Blastocystis subtypes 3 and 4 were inversely correlated with Akkermansia, suggesting differential associations of subtypes with host health.

CONCLUSIONS

These results emphasise the role of Blastocystis as a common constituent of the healthy gut microbiota. We show its prevalence is reduced in patients with active IBD and demonstrate that subtype characterisation is essential for assessing the relationship between Blastocystis, microbiota profile and host health. These findings have direct clinical applications, especially in donor selection for faecal transplantation.

The role of the gut microbiota in development, function and disorders of the central nervous system and the enteric nervous system

The gut microbiota has emerged as an environmental factor that modulates the development of the central nervous system (CNS) and the enteric nervous system (ENS). Before obtaining its own microbiota, eutherian foetuses are exposed to products and metabolites from the maternal microbiota. At birth, the infants are colonised by microorganisms. The microbial composition in early life is strongly influenced by the mode of delivery, the feeding method, the use of antibiotics and the maternal microbial composition. Microbial products and microbially produced metabolites act as signalling molecules that have direct or indirect effects on the CNS and the ENS. An increasing number of studies show that the gut microbiota can modulate important processes during development, including neurogenesis, myelination, glial cell function, synaptic pruning and blood-brain barrier permeability. Furthermore, numerous studies indicate that there is a developmental window early in life during which the gut microbial composition is crucial and perturbation of the gut microbiota during this period causes long-lasting effects on the development of the CNS and the ENS. However, other functions are readily modulated in adult animals, including microglia activation and neuroinflammation. Several neurobehavioural, neurodegenerative, mental and metabolic disorders, including Parkinson disease, autism spectrum disorder, schizophrenia, Alzheimer's disease, depression and obesity, have been linked to the gut microbiota. This review focuses on the role of the microorganisms in the development and function of the CNS and the ENS, as well as their potential role in pathogenesis.

Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France

The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.

Repertoire of bacterial species cultured from the human oral cavity and respiratory tract

While the gut microbiota is currently in the spotlight, the airway microbiome has been recently associated with several pulmonary diseases and carcinogenesis. As there are several biases associated with high-throughput sequencing methods, cultivation techniques are crucial for the investigation of the human microbiome. We thus aimed to build an exhaustive database, including a list of microbes isolated by culture from respiratory specimens, by performing a review of the literature. Herein, we have listed a total of 756 species cultured from the human respiratory tract. This represents 27.23% of the overall bacterial richness captured from human being by culture methods. This repertoire could be valuable for the elucidation of the interactions between the respiratory microbiome and human health.

The gut microbiome and aquatic toxicology: An emerging concept for environmental health

The microbiome plays an essential role in the health and onset of diseases in all animals, including humans. The microbiome has emerged as a central theme in environmental toxicology because microbes interact with the host immune system in addition to its role in chemical detoxification. Pathophysiological changes in the gastrointestinal tissue caused by ingested chemicals and metabolites generated from microbial biodegradation can lead to systemic adverse effects. The present critical review dissects what we know about the impacts of environmental contaminants on the microbiome of aquatic species, with special emphasis on the gut microbiome. We highlight some of the known major gut epithelium proteins in vertebrate hosts that are targets for chemical perturbation, proteins that also directly cross-talk with the microbiome. These proteins may act as molecular initiators for altered gut function, and we propose a general framework for an adverse outcome pathway that considers gut dysbiosis as a major contributing factor to adverse apical endpoints. We present 2 case studies, nanomaterials and hydrocarbons, with special emphasis on the Deepwater Horizon oil spill, to illustrate how investigations into the microbiome can improve understanding of adverse outcomes. Lastly, we present strategies to functionally relate chemical-induced gut dysbiosis with adverse outcomes because this is required to demonstrate cause-effect relationships. Further investigations into the toxicant-microbiome relationship may prove to be a major breakthrough for improving animal and human health. Environ Toxicol Chem 2018;37:2758-2775. © 2018 SETAC.

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing

BACKGROUND

Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.

RESULTS

Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02). Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).

CONCLUSION

Significant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.

Salt-dependent regulation of archaellins in Haloarcula marismortui

Microorganisms require a motility structure to move towards optimal growth conditions. The motility structure from archaea, the archaellum, is fundamentally different from its bacterial counterpart, the flagellum, and is assembled in a similar fashion as type IV pili. The archaellum filament consists of thousands of copies of N‐terminally processed archaellin proteins. Several archaea, such as the euryarchaeon Haloarcula marismortui, encode multiple archaellins. Two archaellins of H. marismortui display differential stability under various ionic strengths. This suggests that these proteins behave as ecoparalogs and perform the same function under different environmental conditions. Here, we explored this intriguing system to study the differential regulation of these ecoparalogous archaellins by monitoring their transcription, translation, and assembly into filaments. The salt concentration of the growth medium induced differential expression of the two archaellins. In addition, this analysis indicated that archaellation in H. marismortui is majorly regulated on the level of secretion, by a still unknown mechanism. These findings indicate that in archaea, multiple encoded archaellins are not completely redundant, but in fact can display subtle functional differences, which enable cells to cope with varying environmental conditions.

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.

Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients

Metabolic syndrome is a cluster of three or more metabolic disorders including insulin resistance, obesity, and hyperlipidemia. Obesity has become the epidemic of the twenty-first century with more than 1.6 billion overweight adults. Due to the strong connection between obesity and type 2 diabetes, obesity has received wide attention with subsequent coining of the term "diabesity." Recent studies have identified unique contributions of the immensely diverse gut microbiota in the pathogenesis of obesity and diabetes. Several mechanisms have been proposed including altered glucose and fatty acid metabolism, hepatic fatty acid storage, and modulation of glucagon-like peptide (GLP)-1. Importantly, the relationship between unhealthy diet and a modified gut microbiota composition observed in diabetic or obese subjects has been recognized. Similarly, the role of diet rich in polyphenols and plant polysaccharides in modulating gut bacteria and its impact on diabetes and obesity have been the subject of investigation by several research groups. Gut microbiota are also responsible for the extensive metabolism of polyphenols thus modulating their biological activities. The aim of this review is to shed light on the composition of gut microbes, their health importance and how they can contribute to diseases as well as their modulation by polyphenols and polysaccharides to control obesity and diabetes. In addition, the role of microbiota in improving the oral bioavailability of polyphenols and hence in shaping their antidiabetic and antiobesity activities will be discussed.

Anticancer effects of the microbiome and its products

The human gut microbiome modulates many host processes, including metabolism, inflammation, and immune and cellular responses. It is becoming increasingly apparent that the microbiome can also influence the development of cancer. In preclinical models, the host response to cancer treatment has been improved by modulating the gut microbiome; this is known to have an altered composition in many diseases, including cancer. In addition, cancer treatment with microbial agents or their products has the potential to shrink tumours. However, the microbiome could also negatively influence cancer prognosis through the production of potentially oncogenic toxins and metabolites by bacteria. Thus, future antineoplastic treatments could combine the modulation of the microbiome and its products with immunotherapeutics and more conventional approaches that directly target malignant cells.

The impact of culturomics on taxonomy in clinical microbiology

Over the past decade, new culture methods coupled to genome and metagenome sequencing have enabled the number of isolated bacterial species with standing in nomenclature to rise to more than 15,000 whereas it was only 1791 in 1980. 'Culturomics', a new approach based on the diversification of culture conditions, has enabled the isolation of more than 1000 distinct human-associated bacterial species since 2012, including 247 new species. This strategy was demonstrated to be complementary to metagenome sequencing for the exhaustive study of the human microbiota and its roles in health and diseases. However, by identifying a large number of new bacterial species in a short time, culturomics has highlighted a need for taxonomic approaches adapted to clinical microbiology that would include the use of modern and reproducible tools, including high throughput genomic and proteomic analyses. Herein, we review the development of culturomics and genomics in the clinical microbiology field and their impact on bacterial taxonomy.

Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2016

A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics creates changes in taxonomy at a logarithmic rate further complicating this process. This update focuses on the description of new species and classification changes proposed in 2016.