Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation

Diverse microbial signatures within the intestinal microbiota have been associated with intestinal and systemic inflammatory diseases, but whether these candidate microbes actively modulate host phenotypes or passively expand within the altered microbial ecosystem is frequently not known. Here we demonstrate that colonization of mice with a member of the genus Prevotella, which has been previously associated to colitis in mice, exacerbates intestinal inflammation. Our analysis revealed that Prevotella intestinalis alters composition and function of the ecosystem resulting in a reduction of short-chain fatty acids, specifically acetate, and consequently a decrease in intestinal IL-18 levels during steady state. Supplementation of IL-18 to Prevotella-colonized mice was sufficient to reduce intestinal inflammation. Hence, we conclude that intestinal Prevotella colonization results in metabolic changes in the microbiota, which reduce IL-18 production and consequently exacerbate intestinal inflammation, and potential systemic autoimmunity.

Identification of Allobaculum mucolyticum as a novel human intestinal mucin degrader

The human gut microbiota plays a central role in intestinal health and disease. Yet, many of its bacterial constituents are functionally still largely unexplored. A crucial prerequisite for bacterial survival and proliferation is the creation and/or exploitation of an own niche. For many bacterial species that are linked to human disease, the inner mucus layer was found to be an important niche. Allobaculum mucolyticum is a newly identified, IBD-associated species that is thought be closely associated with the host epithelium. To explore how this bacterium is able to effectively colonize this niche, we screened its genome for factors that may contribute to mucosal colonization. Up to 60 genes encoding putative Carbohydrate Active Enzymes (CAZymes) were identified in the genome of A. mucolyticum. Mass spectrometry revealed 49 CAZymes of which 26 were significantly enriched in its secretome. Functional assays demonstrated the presence of CAZyme activity in A. mucolyticum conditioned medium, degradation of human mucin O-glycans, and utilization of liberated non-terminal monosaccharides for bacterial growth. The results support a model in which sialidases and fucosidases remove terminal O-glycan sugars enabling subsequent degradation and utilization of carbohydrates for A. mucolyticum growth. A. mucolyticum CAZyme secretion may thus facilitate bacterial colonization and degradation of the mucus layer and may pose an interesting target for future therapeutic intervention.

Purple-leaf tea (Camellia sinensis L.) ameliorates high-fat diet induced obesity and metabolic disorder through the modulation of the gut microbiota in mice

Background

Obesity and its associated diseases have become a major world-wide health problem. Purple-leaf Tea (Camellia sinensis L.) (PLT), that is rich of anthocyanins, has been shown to have preventive effects on obesity and metabolic disorders. The intestinal microbiota has been shown to contribute to inflammation, obesity, and several metabolic disorders. However, whether PLT consumption could prevent obesity and diet-induced metabolic diseases by modulating the gut microbiota, is not clearly understood.

Methods

In this study, six-week-old male C57BL/6 J mice were fed a normal diet (ND) or a high fat diet (HFD) without or with PLT for 10 weeks.

Results

PLT modulated the gut microbiota in mice and alleviated the symptoms of HFD-induced metabolic disorders, such as insulin resistance, adipocyte hypertrophy, and hepatic steatosis. PLT increased the diversity of the microbiota and the ratio of Firmicutes to Bacteroidetes. f_Barnesiellaceae, g_Barnesiella, f_Ruminococcaceae, and f_Lachnospiraceae were discriminating faecal bacterial communities of the PLT mice that differed from the HFD mice.

Conclusions

These data indicate that PLT altered the microbial contents of the gut and prevented microbial dysbiosis in the host, and consequently is involved in the modulation of susceptibility to insulin resistance, hepatic diseases, and obesity that are linked to an HFD.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

Anti-Obesity Effect of Dictyophora indusiata Mushroom Polysaccharide (DIP) in High Fat Diet-Induced Obesity via Regulating Inflammatory Cascades and Intestinal Microbiome

Obesity is a multifactorial metabolic disorder characterized by low-grade chronic inflammation, hyper-permeability of the gut epithelium, and perturbation of the intestinal microbiome. Despite the numerous therapeutic efficacies of Dictyophora indusiata mushroom, its biological activity in alleviating obesity through regulation of the gut microbiota and inflammatory cascades remain obscure. Henceforth, we determined the modulatory impact of D. indusiata polysaccharide (DIP) in the high-fat diet (HFD)-induced obesity mice model. The experimental subjects (BALB/C mice) were supplemented with chow diet (Control group), high-fat diet (HFD group), or HFD along with DIP at a low dose [HFD + DIP(L)] and high dose [HFD + DIP(H)]. Obesity-related parameters, including body weight gain, epididymal adipocyte size, fat accumulation, adipogenic markers, lipogenic markers, inflammatory associated markers, intestinal integrity, and intestinal microbiome, were elucidated. Our findings demonstrated that the oral administration of DIP at low dose partially and at high dose significantly reversed HFD-induced obesity parameters. Furthermore, the body weight, fat accumulation, adipocyte size, adipogenic and liver associated markers, glucose levels, inflammatory cytokines, and endotoxin (Lipopolysaccharide, LPS) levels were reduced considerably. Moreover, the study revealed that DIP treatment reversed the dynamic alterations of the gut microbiome community by decreasing the Firmicutes to Bacteroidetes ratio. These findings led us to infer the therapeutic potential of DIP in alleviating HFD-induced obesity via regulating inflammatory cascades, modulating intestinal integrity and intestinal microbiome community.

Developing a Functional Poly(dimethylsiloxane)-Based Microbial Nanoculture System Using Dimethylallylamine

Here, a novel poly(dimethylsiloxane) (PDMS)-based microbial culture system was investigated. Bacteria were encapsulated in functional and semipermeable membranes, mimicking the cell microenvironment and facilitating mass transport for interrogating microbial dynamics, thereby overcoming one of the major challenges associated with commercially available PDMS such as Sylgard 184. The hydrophobic nature and lack of control in the polymer network in Sylgard 184 significantly impede the the tunability of the transport and mechanical properties of the material as well as its usage as an isolation chamber for culturing and delivering microbes. Therefore, a novel PDMS composition was developed and functionalized with dimethylallylamine (DMAA) to alter its hydrophobicity and modify the polymer network. Characterization techniques including NMR spectroscopy, contact angle measurements, and sol-gel process were utilized to evaluate the physical and chemical properties of the newly fabricated membranes. Furthermore, the DMAA-containing polymer mixture was used as a proof of concept to generate hydrodynamically stable microcapsules and cultivate Escherichia coli cells in the functionalized capsules. The membrane exhibited a selective permeability to tetracycline, which diffused into the capsules to inhibit the growth of the encapsulated microbes. The functionality achieved here with the addition of DMAA, coupled with the high-throughput encapsulation technique, could prove to be an effective testing and diagnostic tool to evaluate microbial resistance, growth dynamics, and interspecies interaction and lays the foundation for in vivo models.

Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach

Determination of metagenome composition is still one of the most interesting problems of bioinformatics. It involves a wide range of mathematical methods, from probabilistic models of combinatorics to cluster analysis and pattern recognition techniques. The successful advance of rapid sequencing methods and fast and precise metagenome analysis will increase the diagnostic value of healthy or pathological human metagenomes. The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study. The approach is based on analysis of the compositional spectra of subsequently sequenced samples of the medium. Its essential feature is using random fluctuations in the bacteria number in different samples of the same metagenome. The possibility of effective implementation of the algorithm in the presence of data errors is also discussed. In the work, the algorithm of a metagenome evaluation is described, including the estimation of the genome number and the identification of the genomes with known compositional spectra. It should be emphasized that evaluating the genome number in a metagenome can be always helpful, regardless of the metagenome separation techniques, such as clustering the sequencing results or marker analysis.

Selective Bacterial Colonization of the Murine Larynx in a Gnotobiotic Model

The larynx is a mucosal organ situated between the respiratory and gastrointestinal tracts. Little is known about microbial contributions to laryngeal epithelial health and pathogenesis. Developing a gnotobiotic laryngeal model will introduce new avenues for targeted explorations of microbes in laryngeal mucosal biology, allowing for enhanced understanding of host-microbe interaction in the upper airway. In this study, we first assessed the potential of using gut microbiota as a source to establish laryngeal microbiota in germ-free mice. Results demonstrated the selective nature of the upper airway and provided evidence that gut bacteria can assemble into communities that resemble the commensal resident bacteria occurring in the larynx of conventionally-raised animals phylogenetically and functionally. Then, we confirmed the reproducibility of laryngeal colonization through comparison of laryngeal microbiota in the larynx along with neighboring regions (base of tongue, esophagus, and trachea) between conventionally-raised and germ-free mice that conventionalized with cecal microbiota. Despite taxonomic differences, the established laryngeal microbiota from cecal content exhibited similarity to commensal resident microbiota in diversity within/between communities and predicted metagenomic functions. Our data also suggests little difference in bacterial distribution across the larynx and its surrounding regions and that cell motility and the ability to degrade xenobiotics is critical for bacteria colonizing upper airway. Successful colonization of laryngeal and oropharyngeal regions with gut microbiota in our study will greatly facilitate the investigation of potential localized inflammatory responses within host tissues that contribute to the disorders of essential laryngeal functions. Utilizing said gnotobiotic model to conduct future studies will allow for novel insights into direct microbial contributions to laryngeal epithelial health and pathogenesis.

Monitoring the Diversity and Metabolic Shift of Gut Microbes during Green Tea Feeding in an In Vitro Human Colonic Model

The human gut microbiome plays an important role in human health, and many factors such as environment, host genetics, age, and diet have been found to influence the microbial composition. Tea, as one of the widely consumed beverages, has been known for centuries to have antioxidant, anti-inflammatory, and anticancer effects. To investigate the impact of green tea polyphenol on the diversity and metabolic functions of human gut microbes, we applied an in vitro human colonic model (HCM) in this study to mimic a short-term green tea ingestion event and investigate its related changes to gut microbial composition and their metabolic functions. The pH, temperature, anaerobic environment, feeding nutrient, and time point in each compartment of the HCM were tightly controlled to simulate the intestinal system, and pooled human fecal samples of two healthy volunteers were used for the colon microbiota inoculation within the colonic model. By adding green tea extract (GTE) to the growth medium, the detailed impacts of GTE polyphenol on gut microbial population/diversity, gut microbial metabolites, metabolic pathways, and their associations were investigated via 16 S ribosomal DNA sequencing and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses. Our data indicated that the treatment of green tea extract applied to gut microbiota can induce a significant decrease in the abundance of Firmicutes and a slight decrease in the abundance of Bacteroidetes, and these changes result in a decreased Firmicutes/Bacteroidetes ratio, which can be an effective indicator for successful GTE intervention, which may generate beneficial health effect to human. Meanwhile, the relative abundances of many detected bacteria genera among three HCM vessels changed through the GTE intervention. The overall effects of GTE on gut microbial beta-diversity were observed by multivariate statistical analyses, and the differences in metabolic profiles from different GTE treatment stages were detected. Moreover, we identified several associations between microbial population and microbial metabolites, which may assist us in establishing new hypotheses for future related studies. In summary, our study suggested that the microbial compositional changes induced by GTE also changed their metabolic functions, and consequentially, may change the host metabolism and impact human health.

Applications of Human Skin Microbiota in the Cutaneous Disorders for Ecology-Based Therapy

The skin represents the exterior interface between the human body with the environment while providing a home to trillions of the commensal microorganisms—collectively referred to as the skin microbiota. These microbes that coexist in an established balance play a pivotal role in the protection of cutaneous health and the orchestration of skin homeostasis. However, the well-controlled but delicate balance can be perturbed by alterations in the skin microbial communities, namely, dysbiosis, often due to commensals defeated by pathogens competing for space and nutrients, which leads to the occurrence of multiple cutaneous disorders. In view of this, the analysis of skin microbiota constituents in skin diseases is crucial for defining the role of commensal microbes and treatment of skin diseases. Emerging evidence shows that the ecology-based therapy of microbial transplantation has been proven as a valid therapeutic strategy for cutaneous disorders caused by skin microbial dysbiosis. Although its mechanism is not well-understood, there are already some applications for ecology-based therapy with the aim of correcting the imbalances on the cutaneous ecosystem. In this review, we summarize the interactions between dysbiosis and the cutaneous disorders, including homeostasis and dysbiosis of skin microbiota, microbial composition in skin diseases, and the mechanisms and applications of reversing or ameliorating the dysbiosis by the targeted manipulation of the skin microbiota, which may contribute to aid development of therapeutic modality for ecology-based therapy.

Sharing a β-Glucan Meal: Transcriptomic Eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi Consortium

Whole-transcriptome analysis was used to investigate the molecular interplay between three bacterial species that are members of the human gut microbiota. Bacteroides ovatus, Subdoligranulum variabile, and Hungatella hathewayi formed associations in cocultures fed barley β-glucan, a constituent of dietary fiber. B. ovatus depolymerized β-glucan and released, but did not utilize, 3-O-β-cellobiosyl-d-glucose (DP3) and 3-O-β-cellotriosyl-d-glucose (DP4). These oligosaccharides provided growth substrates for S. variabile and H. hathewayi with a preference for DP4 in the case of the latter species. There was increased transcription of a B. ovatus mixed-linkage-β-glucan utilization locus, as well as carbohydrate transporters in S. variabile and H. hathewayi when in batch coculture. Increased transcription of the β-glucan utilization locus did not occur in continuous culture. Evidence for interactions relating to provision of cobalamin, alterations to signaling, and modulation of the "stringent response" (an adaptation to nutrient deprivation) were detected. Overall, we established a bacterial consortium based on barley β-glucan in vitro, which can be used to investigate aspects of the functional blueprint of the human gut microbiota.IMPORTANCE The microbial community, mostly composed of bacterial species, residing in the human gut degrades and ferments polysaccharides derived from plants (dietary fiber) that would not otherwise be digested. In this way, the collective metabolic actions of community members extract additional energy from the human diet. While the variety of bacteria present in the microbial community is well known, the formation of bacterial consortia, and the consequent interactions that result in the digestion of dietary polysaccharides, has not been studied extensively. The importance of our work was the establishment, under laboratory conditions, of a consortium of gut bacteria that formed around a dietary constituent commonly present in cereals. This enabled the metabolic interplay between the bacterial species to be studied. This kind of knowledge is required to construct an interactive, metabolic blueprint of the microbial community that inhabits the human gut.

Strain-level epidemiology of microbial communities and the human microbiome

The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.

Evolving Technologies in Gastrointestinal Microbiome Era and Their Potential Clinical Applications

The human gastrointestinal microbiota (GIM) is a complex and diverse ecosystem that consists of community of fungi, viruses, protists and majorly bacteria. The association of several human illnesses, such as inflammatory bowel disease, allergy, metabolic syndrome and cancers, have been linked directly or indirectly to compromise in the integrity of the GIM, for which some medical interventions have been proposed or attempted. This review highlights and gives update on various technologies, including microfluidics, high-through-put sequencing, metabolomics, metatranscriptomics and culture in GIM research and their applications in gastrointestinal microbiota therapy, with a view to raise interest in the evaluation, validation and eventual use of these technologies in diagnosis and the incorporation of therapies in routine clinical practice.

Non-Melanoma Skin Cancer: news from microbiota research

Recently, research has been deeply focusing on the role of the microbiota in numerous diseases, either affecting the skin or other organs. What it is well established is that its dysregulation promotes several cutaneous disorders (i.e. psoriasis and atopic dermatitis). To date, little is known about its composition, mediators and role in the genesis, progression and response to therapy of Non-Melanoma Skin Cancer (NMSC). Starting from a bibliographic study, we classified the selected articles into four sections: i) normal skin microbiota; ii) in vitro study models; iii) microbiota and NMSC and iv) probiotics, antibiotics and NMSC. What has emerged is how skin microflora changes, mainly represented by increases of Staphylococcus aureus, Streptococcus pyogenes and Pseudomonas aeruginosa strains, modifications in the mutual quantity of β-Human papillomavirus genotypes, of Epstein Barr Virus and Malassezia or candidiasis, may contribute to the induction of a state of chronic self-maintaining inflammation, leading to cancer. In this context, the role of S. aureus and that of specific antimicrobial peptides look to be prominent. Moreover, although antibiotics may contribute to carcinogenesis, due to their ability to influence the microbiota balance, specific probiotics, such as Lacticaseibacillus rhamnosus GG, Lactobacillus johnsonii NCC 533 and Bifidobacteria spp., may be protective.

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture

Bacterial culture and assay are components of basic microbiological research, drug development, and diagnostic screening. However, community diversity can make it challenging to comprehensively perform experiments involving individual microbiota members. Here, we present a new microfluidic culture platform that makes it feasible to measure the growth and function of microbiota constituents in a single set of experiments. As a proof of concept, we demonstrate how the platform can be used to measure how hundreds of gut bacterial taxa drawn from different people metabolize dietary carbohydrates. Going forward, we expect this microfluidic technique to be adaptable to a range of other microbial assay needs.

Culture and screening of gut bacteria enable testing of microbial function and therapeutic potential. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for separating and assaying growth of microbiota members in picoliter droplets (MicDrop). MicDrop enabled us to cultivate 2.8 times more bacterial taxa than typical batch culture methods. We then used MicDrop to test whether individuals possess similar abundances of carbohydrate-degrading gut bacteria, using an approach which had previously not been possible due to throughput limitations of traditional bacterial culture techniques. Single MicDrop experiments allowed us to characterize carbohydrate utilization among dozens of gut bacterial taxa from distinct human stool samples. Our aggregate data across nine healthy stool donors revealed that all of the individuals harbored gut bacterial species capable of degrading common dietary polysaccharides. However, the levels of richness and abundance of polysaccharide-degrading species relative to monosaccharide-consuming taxa differed by up to 2.6-fold and 24.7-fold, respectively. Additionally, our unique dataset suggested that gut bacterial taxa may be broadly categorized by whether they can grow on single or multiple polysaccharides, and we found that this lifestyle trait is correlated with how broadly bacterial taxa can be found across individuals. This demonstration shows that it is feasible to measure the function of hundreds of bacterial taxa across multiple fecal samples from different people, which should in turn enable future efforts to design microbiota-directed therapies and yield new insights into microbiota ecology and evolution.

IMPORTANCE Bacterial culture and assay are components of basic microbiological research, drug development, and diagnostic screening. However, community diversity can make it challenging to comprehensively perform experiments involving individual microbiota members. Here, we present a new microfluidic culture platform that makes it feasible to measure the growth and function of microbiota constituents in a single set of experiments. As a proof of concept, we demonstrate how the platform can be used to measure how hundreds of gut bacterial taxa drawn from different people metabolize dietary carbohydrates. Going forward, we expect this microfluidic technique to be adaptable to a range of other microbial assay needs.

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

The human gut microbiome harbors hundreds of bacterial species with diverse biochemical capabilities. Dozens of drugs have been shown to be metabolized by single isolates from the gut microbiome, but the extent of this phenomenon is rarely explored in the context of microbial communities. Here, we develop a quantitative experimental framework for mapping the ability of the human gut microbiome to metabolize small molecule drugs: Microbiome-Derived Metabolism (MDM)-Screen. Included are a batch culturing system for sustained growth of subject-specific gut microbial communities, an ex vivo drug metabolism screen, and targeted and untargeted functional metagenomic screens to identify microbiome-encoded genes responsible for specific metabolic events. Our framework identifies novel drug-microbiome interactions that vary between individuals and demonstrates how the gut microbiome might be used in drug development and personalized medicine.

Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

Biotransformation of dietary phytoestrogens by gut microbes: A review on bidirectional interaction between phytoestrogen metabolism and gut microbiota

Phytoestrogens are a class of plant produced polyphenolic compounds with diphenolic structure, which is similar to 17β-estradiol. These phytoestrogens preferentially bind to estrogen receptors, however, with weak affinity. Recently, many studies have found that these phytoestrogens can be transformed by gut microbiota through novel enzymatic reactions into metabolites with altered bioactivity. Recent studies have also implied that these metabolites could possibly modulate the host gut ecosystem, gene expression, metabolism and the immune system. Thus, isolating gut microbes capable of biotransforming phytoestrogens and characterizing the novel enzymatic reactions involved are principal to understand the mechanisms of beneficial effects brought by gut microbiota and their metabolism on phytoestrogens, and to provide the theoretical knowledge for the development of functional probiotics. In the present review, we summarized works on gut microbial biotransformation of phytoestrogens, including daidzin (isoflavone), phenylnaringenin (prenylflavonoid), lignans, resveratrol (stilbene) and ellagitannins. We mainly focus on gut bacterial isolation, metabolic pathway characterization, and the bidirectional interaction of phytoestrogens with gut microbes to illustrate the novel metabolic capability of gut microbiota and the methods used in these studies.

Tn-Seq reveals hidden complexity in the utilization of host-derived glutathione in Francisella tularensis

Host-derived glutathione (GSH) is an essential source of cysteine for the intracellular pathogen Francisella tularensis. In a comprehensive transposon insertion sequencing screen, we identified several F. tularensis genes that play central and previously unappreciated roles in the utilization of GSH during the growth of the bacterium in macrophages. We show that one of these, a gene we named dptA, encodes a proton-dependent oligopeptide transporter that enables growth of the organism on the dipeptide Cys-Gly, a key breakdown product of GSH generated by the enzyme γ-glutamyltranspeptidase (GGT). Although GGT was thought to be the principal enzyme involved in GSH breakdown in F. tularensis, our screen identified a second enzyme, referred to as ChaC, that is also involved in the utilization of exogenous GSH. However, unlike GGT and DptA, we show that the importance of ChaC in supporting intramacrophage growth extends beyond cysteine acquisition. Taken together, our findings provide a compendium of F. tularensis genes required for intracellular growth and identify new players in the metabolism of GSH that could be attractive targets for therapeutic intervention.

Surface Modifications for Improved Delivery and Function of Therapeutic Bacteria

Live therapeutic bacteria (LTBs) hold promise to treat microbiome-related diseases. However, few approaches to improve the colonization of LTBs in the gastrointestinal tract exist, despite colonization being a prerequisite for efficacy of many LTBs. Here, a modular platform to rapidly modify the surface of LTBs to enable receptor-specific interactions with target surfaces is reported. Inspired by bacterial adhesins that facilitate colonization, synthetic adhesins (SAs) are developed for LTBs in the form of antibodies conjugated to their surface. The SA platform is nontoxic, does not alter LTB growth kinetics, and can be used with any antibody or bacterial strain combination. By improving adhesion, SA-modified bacteria demonstrate enhanced in vitro pathogen exclusion from cell monolayers. In vivo kinetics of SA-modified LTBs is tracked in the feces and intestines of treated mice, demonstrating that SA-modified bacteria alter short-term intestinal transit and improve LTB colonization and pharmacokinetics. This platform enables rapid formation of an intestinal niche, leading to an increased maximum concentration and a 20% improvement in total LTB exposure. This work is the first application of traditional pharmacokinetic analysis to design and evaluate LTB drug delivery systems and provides a platform toward controlling adhesion, colonization, and efficacy of LTBs.

Draft Genome Sequences of Two Clostridium Isolates from the Poultry Gastrointestinal Tract

Here, we announce the draft genome sequences of two Clostridium strains, C8-1-8 and C2-6-12, isolated from the cecal contents of commercial broiler chickens (in Athens, GA). These strains may represent potentially novel species within the genus Clostridium, and these draft genomes allow further investigation into potential probiotics for poultry.

Here, we announce the draft genome sequences of two Clostridium strains, C8-1-8 and C2-6-12, isolated from the cecal contents of commercial broiler chickens (in Athens, GA). These strains may represent potentially novel species within the genus Clostridium, and these draft genomes allow further investigation into potential probiotics for poultry.

Gut Microbiota and Disorders of the Central Nervous System

The gut microbiota, consisting of bacteria, fungi, archaea, viruses, and protozoa, together with their collective genomes (microbiome), plays a key role in immune system development and maturation, gut morphology, and in performing essential metabolic functions. Several factors, including lifestyle, body mass index, diet, antibiotic use, and the environment, influence the balance of the intestinal microbiota, whose alterations (the so-called dysbiosis) in recent years have been associated with the onset and/or progression of neurological and neuropsychiatric disorders. The purpose of this narrative review is to provide an overview of the possible involvement of the microbiota-gut-brain axis in the pathogenesis of diseases of the central nervous system, with a special focus on key issues and common misjudgments on the potential contribution of specific microorganisms.

Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities

Phylosymbiosis, where similarities in host-associated microbial communities recapitulate the phylogeny of their hosts, is a newly recognized yet pervasive pattern in the field of host-microbe interactions. While phylosymbiosis has been documented across many systems, we still have a poor understanding of the mechanisms that underlie this emergent pattern. Host selection of the microbiome is a widely cited mechanism, yet other basic ecological and evolutionary processes (dispersal, drift and diversification) may also be at play. This paper discusses the roles that each of these processes and their interactions may play in yielding phylosymbiotic signals across hosts. Finally, this paper will identify open questions and methods that are required to better understand the relative contributions of these basic processes to phylosymbiosis. Given that phylosymbiosis has been shown to relate to functional components of host fitness, understanding the processes that contribute to these patterns will be important for our understanding of the ecology and evolution of host-microbe interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Evaluating the Impact of Four Major Nutrients on Gut Microbial Metabolism by a Targeted Metabolomics Approach

Gut microbiome plays fundamental roles in host physiology, and gut microbial metabolism is important to the host-microbiome homeostasis. As major contributors to gut microbial metabolism, the medium nutritional components are essential to in vitro gut microbiome growths, and four nutrients, namely, inorganic salts, bile salts, short-chain fatty acids (SCFAs), and mucin, have gained particular attention because of their significant variation found in different growth environments and their ability to modulate the gut microbial population and functions. However, a systematic study is lacking to evaluate the effects of these four nutrients on the gut microbiome in terms of their impact on the microbial metabolic profiles. To fill the gap of the knowledge, we applied mass-spectrometry-based targeted metabolomics approach to study the regulation effects of these four medium components on in vitro-cultured gut microbiota. Our results show that inorganic salts and mucin had the greatest impacts on the gut microbiome metabolic profile compared to the other components studied, with gut microbial cultures grown with low-concentration inorganic salts and mucin-supplemented medium demonstrating greater numbers of metabolites detected. We also applied metabolic pathway impact analysis, which revealed several significantly impacted metabolic pathways during the comparison of different medium supplements, which could further assist our understanding of the overall impacts of certain critical nutrients on gut microbial metabolism. In summary, this pilot study can serve as a first attempt to evaluate the individual nutritional component in their contribution to gut microbial metabolic functions.

Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices

The development of next-generation sequencing technology has enabled researchers to explore and understand the gut microbiome from a broader and deeper perspective. However, the results of different studies on gut microbiota are highly variable even in the same disease, which makes it difficult to guide clinical diagnosis and treatment. The ideal sampling method should be non-invasive, involve little cross-contamination or bowel preparation, and collect gut microbiota at different sites. Currently, sequencing technologies are usually based on samples collected from feces, mucosal biopsy, intestinal fluid, etc. However, different parts of the gastrointestinal tract possess various physiological characteristics that are essential for particular species of living microbiota. Moreover, current sampling methods are somewhat defective. For example, fecal samples are just a proxy for intestinal microbiota, while biopsies are invasive for patients and not suitable for healthy controls. In this review, we summarize the current sampling methods and their advantages and shortcomings. New sampling technologies, such as the Brisbane Aseptic Biopsy Device and the intelligent capsule, are also mentioned to inspire the development of future precise description methods of the gut microbiome.

Reduced anti-inflammatory gut microbiota are associated with depression and anhedonia

INTRODUCTION

Characterise gut microbiota distributions of participants with co-occurring depression and anxiety, in those with only depression or with anxiety, and determine if gut bacteria differentially correlates with distinct clinical presentations.

METHODS

Participants (10 healthy controls [mean age: 33, 60% female] and 60 psychiatric subjects; major depressive disorder (comorbid with anxiety), n = 38 [mean age: 39.2, 82% female], anxiety only, n = 8 [mean age: 40.0, 100% female], depression only without anxiety, n = 14 [mean age: 41.9, 79% female]) were characterized by psychiatric assessments. Quantitative PCR and 16S rRNA sequencing were used to characterize the gut microbiota in stool samples.

RESULTS

Altered microbiota correlated with pre-defined clinical presentation, with Bacteroides (p = 0.011) and the Clostridium leptum subgroup (p = 0.023) significantly different between clinical categories. Cluster analysis of the total sample using weighted UniFrac β-diversity of the gut microbiota identified two different clusters defined by differences in bacterial distribution. Cluster 2 had higher Bacteroides (p = 0.006), and much reduced presence of Clostridales (p<0.001) compared to Cluster 1. Bifidobacterium (p = 0.0173) was also reduced in Cluster 2 compared to Cluster 1. When evaluated for clinical charateristics, anhedonia scores in Cluster 2 were higher than in Cluster 1.

LIMITATIONS

The sample is smaller and predominately female.

CONCLUSIONS

Reduced or absent Clostridia was consistently seen in those with depression, independent of the presence of anxiety. Conversely, reduced Bacteroides may be more associated with the presence of anxiety, independent of the presence of depression. These differences suggest that gut microbiota distribution could help clarify the underlying pathology of comorbid clinical presentation.

Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

The scaling of organelles with cell size is thought to be exclusive to eukaryotes. Here, we demonstrate that similar scaling relationships hold for the bacterial nucleoid. Despite the absence of a nuclear membrane, nucleoid size strongly correlates with cell size, independent of changes in DNA amount and across various nutrient conditions. This correlation is observed in diverse bacteria, revealing a near-constant ratio between nucleoid and cell size for a given species. As in eukaryotes, the nucleocytoplasmic ratio in bacteria varies greatly among species. This spectrum of nucleocytoplasmic ratios is independent of genome size, and instead it appears linked to the average population cell size. Bacteria with different nucleocytoplasmic ratios have a cytoplasm with different biophysical properties, impacting ribosome mobility and localization. Together, our findings identify new organizational principles and biophysical features of bacterial cells, implicating the nucleocytoplasmic ratio and cell size as determinants of the intracellular organization of translation.

A sparse covarying unit that describes healthy and impaired human gut microbiota development

Characterizing the organization of the human gut microbiota is a formidable challenge given the number of possible interactions between its components. Using a statistical approach initially applied to financial markets, we measured temporally conserved covariance among bacterial taxa in the microbiota of healthy members of a Bangladeshi birth cohort sampled from 1 to 60 months of age. The results revealed an “ecogroup” of 15 covarying bacterial taxa that provide a concise description of microbiota development in healthy children from this and other low-income countries, and a means for monitoring community repair in undernourished children treated with therapeutic foods. Features of ecogroup population dynamics were recapitulated in gnotobiotic piglets as they transitioned from exclusive milk feeding to a fully weaned state consuming a representative Bangladeshi diet.

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

Secondary bile acids (SBAs) are derived from primary bile acids (PBAs) in a process reliant on biosynthetic capabilities possessed by few microbes. To evaluate the role of BAs in intestinal inflammation, we performed metabolomic, microbiome, metagenomic, and transcriptomic profiling of stool from ileal pouches (surgically created resevoirs) in colectomy-treated patients with ulcerative colitis (UC) versus controls (familial adenomatous polyposis [FAP]). We show that relative to FAP, UC pouches have reduced levels of lithocholic acid and deoxycholic acid (normally the most abundant gut SBAs), genes required to convert PBAs to SBAs, and Ruminococcaceae (one of few taxa known to include SBA-producing bacteria). In three murine colitis models, SBA supplementation reduces intestinal inflammation. This anti-inflammatory effect is in part dependent on the TGR5 bile acid receptor. These data suggest that dysbiosis induces SBA deficiency in inflammatory-prone UC patients, which promotes a pro-inflammatory state within the intestine that may be treated by SBA restoration.

Comprehensive amelioration of high-fat diet-induced metabolic dysfunctions through activation of the PGC-1α pathway by probiotics treatment in mice

Although the beneficial effects of probiotics in the prevention or treatment of metabolic disorders have been extensively researched, the precise mechanisms by which probiotics improve metabolic homeostasis are still not clear. Given that probiotics usually exert a comprehensive effect on multiple metabolic disorders, defining a concurrent mechanism underlying the multiple effects is critical to understand the function of probiotics. In this study, we identified the SIRT1-dependent or independent PGC-1α pathways in multiple organs that mediate the protective effects of a strain of Lactobacillus plantarum against high-fat diet-induced adiposity, glucose intolerance, and dyslipidemia. L. plantarum treatment significantly enhanced the expression of SIRT1, PPARα, and PGC-1α in the liver and adipose tissues under HFD-fed condition. L. plantarum treated mice also exhibited significantly increased expressions of genes involved in bile acid synthesis and reverse cholesterol transport in the liver, browning and thermogenesis of adipose tissue, and fatty acid oxidation in the liver and adipose tissue. Additionally, L. plantarum treatment significantly upregulated the expressions of adiponectin in adipose tissue, irisin in skeletal muscle and subcutaneous adipose tissue (SAT), and FGF21 in SAT. These beneficial changes were associated with a significantly improved HFD-induced alteration of gut microbiota. Our findings suggest that the PGC-1α-mediated pathway could be regarded as a potential target in the development of probiotics-based therapies for the prevention and treatment of metabolic disorders.

Structural modulation of gut microbiota during alleviation of non-alcoholic fatty liver disease with Gynostemma pentaphyllum in rats

Background

The current work aimed to assess whether Gynostemma pentaphyllum (GP), a Chinese herbal medicine, structurally modifies the gut microbiota in rats during non-alcoholic fatty liver disease (NAFLD) treatment.

Methods

High-fat diet (HFD)-induced NAFLD rats were orally administered water decoction of GP or equal amounts of distilled water per day for 4 weeks. Liver tissues were examined by histopathological observation, while intestinal tissues were examined by both histopathological and ultrastructural observations. The levels of fasting blood glucose (FBG), fasting serum insulin (FINS), total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), alanine transaminase (ALT) and aspartate transaminase (AST) were measured by enzymatic method. The levels of toll-like receptor 4 (TLR-4), tumor necrosis factor-alpha (TNF-α), interleukin-1-beta (IL-1β) and interleukin-6 (IL-6) in both serum and hepatic tissues were measured by RT-qPCR. The protein expression level of TLR-4 in hepatic tissues was detected by western blot. The gut microbiota was assessed by 16S rRNA-based microbiota analysis.

Results

GP maintained intestinal integrity and reversed gut dysbiosis in high-fat diet (HFD)-induced NAFLD rats. This also reduced the ratio of Firmicutes to Bacteroidetes, enriching the abundance of beneficial bacteria (Lactococcus spp.) and inhibiting the abundance of pathogenic bacteria (Ruminococcus spp.) in the gut. The levels of pro-inflammatory cytokines (TNF-α, IL-1β and IL-6) and the expression of TLR4 were downregulated (P < 0.05), while the insulin resistance index, HOMA-IR showed improvement by GP treatment (P < 0.05). Liver function indicators (ALT and AST) were remarkably decreased (P < 0.01). Besides, GP treatment reduced TG and LDL-C levels (P < 0.05), and increased HDL-C level (P < 0.05) compared with NAFLD group.

Conclusion

The structural alterations of gut microbiota induced by GP are associated with NAFLD alleviation.

Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly

A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious levels. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1,590 isolates belonging to 102 species. This culture collection represents 34.57% of the taxonomic diversity and 70% functional capacity, as estimated by metagenomic sequencing of the fecal samples used for culture. Using whole-genome sequencing, we characterized species representatives from this collection and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profiles and short-chain fatty acid production. When screened with a coculture assay, 66 species in our culture collection inhibited Clostridioides difficile Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol, or succinate, correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile We tested 256 combinations and found that both species composition and blend size were important in inhibition. Our results show that the interaction of bacteria with one another in a mix and with other members of gut commensals must be investigated to design defined bacterial mixes for inhibiting C. difficile in vivo IMPORTANCE Antibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. The C. difficile-inhibiting species and bacterial combinations identified herein improve the understanding of the ecological interactions controlling colonization resistance against C. difficile and could aid in the design of defined bacteriotherapy as a nonantibiotic alternative against CDI.

Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota

Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity-including of low-abundance taxa-with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.

Understanding immune-microbiota interactions in the intestine

The past two decades have seen an explosion in research that aims to understand how the dynamic interplay with the gut microbiota impacts host health and disease, establishing a role for the gut microbiota in a plethora of pathologies. Understanding how health-promoting microbiota are established and how beneficial host-microbiota interactions are maintained is of immense biomedical importance. Despite the enormous progress that has been made, our knowledge of the specific microbiota members that mediate these effects and the mechanisms underlying these interactions is rudimentary. The dearth of information regarding the nature of advantageous host-microbiota interactions, and the factors that cause these relationships to go awry, has hampered our ability to realize the therapeutic potential of the microbiota. Here we discuss key issues that limit current knowledge and describe a path forwards to improving our understanding of the contributions of the microbiota to host health.

Unsaturated alginate oligosaccharides attenuated obesity-related metabolic abnormalities by modulating gut microbiota in high-fat-diet mice

A new potent prebiotic oligosaccharide for obesity and related metabolic abnormalities by modulating gut microbiota.

Microbiome as an Immunological Modifier

Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.

Physiological and Metabolic Effects of Yellow Mangosteen (Garcinia dulcis) Rind in Rats with Diet-Induced Metabolic Syndrome

Metabolic syndrome is a cluster of disorders that increase the risk of cardiovascular disease and diabetes. This study has investigated the responses to rind of yellow mangosteen (Garcinia dulcis), usually discarded as waste, in a rat model of human metabolic syndrome. The rind contains higher concentrations of phytochemicals (such as garcinol, morelloflavone and citric acid) than the pulp. Male Wistar rats aged 8-9 weeks were fed either corn starch diet or high-carbohydrate, high-fat diet for 16 weeks, which were supplemented with 5% freeze-dried G. dulcis fruit rind powder during the last 8 weeks. We characterised metabolic, cardiovascular, liver and gut microbiota parameters. High-carbohydrate, high-fat diet-fed rats developed abdominal obesity, hypertension, increased left ventricular diastolic stiffness, decreased glucose tolerance, fatty liver and reduced Bacteroidia with increased Clostridia in the colonic microbiota. G. dulcis fruit rind powder attenuated these changes, improved cardiovascular and liver structure and function, and attenuated changes in colonic microbiota. G. dulcis fruit rind powder may be effective in metabolic syndrome by appetite suppression, inhibition of inflammatory processes and increased fat metabolism, possibly related to changes in the colonic microbiota. Hence, we propose the use of G. dulcis fruit rind as a functional food to ameliorate symptoms of metabolic syndrome.

Long-term impact of fecal transplantation in healthy volunteers

BACKGROUND

Fecal microbiota transplantation (FMT) has been recently approved by FDA for the treatment of refractory recurrent clostridial colitis (rCDI). Success of FTM in treatment of rCDI led to a number of studies investigating the effectiveness of its application in the other gastrointestinal diseases. However, in the majority of studies the effects of FMT were evaluated on the patients with initially altered microbiota. The aim of our study was to estimate effects of FMT on the gut microbiota composition in healthy volunteers and to monitor its long-term outcomes.

RESULTS

We have performed a combined analysis of three healthy volunteers before and after capsule FMT by evaluating their general condition, adverse clinical effects, changes of basic laboratory parameters, and several immune markers. Intestinal microbiota samples were evaluated by 16S rRNA gene and shotgun sequencing. The data analysis demonstrated profound shift towards the donor microbiota taxonomic composition in all volunteers. Following FMT, all the volunteers exhibited gut colonization with donor gut bacteria and persistence of this effect for almost ∼1 year of observation. Transient changes of immune parameters were consistent with suppression of T-cell cytotoxicity. FMT was well tolerated with mild gastrointestinal adverse events, however, one volunteer developed a systemic inflammatory response syndrome.

CONCLUSIONS

The FMT leads to significant long-term changes of the gut microbiota in healthy volunteers with the shift towards donor microbiota composition and represents a relatively safe procedure to the recipients without long-term adverse events.

Detecting Changes in the Caenorhabditis elegans Intestinal Environment Using an Engineered Bacterial Biosensor

Caenorhabditis elegans has become a key model organism within biology. In particular, the transparent gut, rapid growing time, and ability to create a defined gut microbiota make it an ideal candidate organism for understanding and engineering the host microbiota. Here we present the development of an experimental model that can be used to characterize whole-cell bacterial biosensors in vivo. A dual-plasmid sensor system responding to isopropyl β-d-1-thiogalactopyranoside was developed and fully characterized in vitro. Subsequently, we show that the sensor was capable of detecting and reporting on changes in the intestinal environment of C. elegans after introducing an exogenous inducer into the environment. The protocols presented here may be used to aid the rational design of engineered bacterial circuits, primarily for diagnostic applications. In addition, the model system may serve to reduce the use of current animal models and aid in the exploration of complex questions within general nematode and host-microbe biology.

Optimization of Culturomics Strategy in Human Fecal Samples

Most bacteria in the human gut are difficult to culture, and culturomics has been designed to overcome this issue. Culturomics makes it possible to obtain living bacteria for further experiments, unlike metagenomics. However, culturomics is work-intensive, which prevents its wide application. In this study, we performed a 30-day continuous enrichment in blood culture bottles and cultured bacterial isolates from pre-cultures removed at different time points. We compared the bacteria isolated from the enriched culture with or without adding fresh medium after each pre-culture was removed. We also compared “experienced” colony picking (i.e., picking two to three colonies for each recognized colony type) and picking all the colonies from each plate. In total, from five fecal samples, 106 species were isolated, including three novel species and six that have not previously been isolated from the human body. Adding fresh medium to the culture increased the rate of bacterial species isolation by 22% compared with the non-supplemented culture. Picking all colonies increased the rate of bacterial isolation by only 8.5% compared with experienced colony picking. After optimization through statistical analysis and simulation, sampling aerobic and anaerobic enrichment cultures at six and seven time-points, respectively, is likely to isolate >90% of bacterial species, reducing the workload by 40%. In conclusion, an extended enrichment step ensures isolation of different bacterial species at different time-points, while adding the same quantity of fresh medium after sampling, the experienced picking and the optimized time-points favor the chance of isolating more bacterial species with less work.

Non-antibiotic Small-Molecule Regulation of DHFR-Based Destabilizing Domains In Vivo

The E. coli dihydrofolate reductase (DHFR) destabilizing domain (DD), which shows promise as a biologic tool and potential gene therapy approach, can be utilized to achieve spatial and temporal control of protein abundance in vivo simply by administration of its stabilizing ligand, the routinely prescribed antibiotic trimethoprim (TMP). However, chronic TMP use drives development of antibiotic resistance (increasing likelihood of subsequent infections) and disrupts the gut microbiota (linked to autoimmune and neurodegenerative diseases), tempering translational excitement of this approach in model systems and for treating human diseases. Herein, we identified a TMP-based, non-antibiotic small molecule, termed 14a (MCC8529), and tested its ability to control multiple DHFR-based reporters and signaling proteins. We found that 14a is non-toxic and can effectively stabilize DHFR DDs expressed in mammalian cells. Furthermore, 14a crosses the blood-retinal barrier and stabilizes DHFR DDs expressed in the mouse eye with kinetics comparable to that of TMP (≤6 h). Surprisingly, 14a stabilized a DHFR DD in the liver significantly better than TMP did, while having no effect on the mouse gut microbiota. Our results suggest that alternative small-molecule DHFR DD stabilizers (such as 14a) may be ideal substitutes for TMP in instances when conditional, non-antibiotic control of protein abundance is desired in the eye and beyond.

Environmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in Mice

Exposure to environmental chemicals during windows of development is a potentially contributing factor in gut microbiota dysbiosis and linked to chronic diseases and developmental disorders. We used a community-level model of microbiota metabolism to investigate the effects of diethylhexyl phthalate (DEHP), a ubiquitous plasticizer implicated in neurodevelopmental disorders, on the composition and metabolite outputs of gut microbiota in young mice. Administration of DEHP by oral gavage increased the abundance of Lachnoclostridium, while decreasing Clostridium sensu stricto Addition of DEHP to in vitro-cultured cecal microbiota increased the abundance of Paenibacillus and Lachnoclostridium Untargeted metabolomics showed that DEHP broadly altered the metabolite profile in the culture. Notably, DEHP enhanced the production of p-cresol while inhibiting butyrate synthesis. Metabolic model-guided correlation analysis indicated that the likely sources of p-cresol are Clostridium species. Monoculture of Lachnoclostridium bolteae confirmed that it is capable of producing p-hydroxyphenylacetic acid, the immediate precursor of p-cresol, and that the species' growth is enhanced upon DEHP exposure. Taken together, these findings suggest a model where DEHP increases production of p-cresol, a bacterial metabolite linked with neurodevelopmental disorders, by expanding the abundance of species that synthesize the metabolite's precursor.IMPORTANCE Several previous studies have pointed to environmental chemical exposure during windows of development as a contributing factor in neurodevelopmental disorders and correlated these disorders with microbiota dysbiosis; however, little is known about how the chemicals specifically alter the microbiota to interfere with development. The findings reported in this paper unambiguously establish that a pollutant linked with neurodevelopmental disorders can directly modify the microbiota to promote the production of a potentially toxic metabolite (p-cresol) that has also been correlated with neurodevelopmental disorders. Furthermore, we used a novel modeling strategy to identify the responsible enzymes and bacterial sources of this metabolite. To the best of our knowledge, the present study is the first to characterize the functional consequence of phthalate exposure on a developed microbiota. Our results suggest that specific bacterial pathways could be developed as diagnostic and therapeutic targets against health risks posed by ingestion of environmental chemicals.

Sinapine reduces non-alcoholic fatty liver disease in mice by modulating the composition of the gut microbiota

Non-alcoholic fatty liver disease (NAFLD) is associated with low-grade chronic inflammation and intestinal dysbiosis. In this study, we investigated the potential benefits of sinapine, a rapeseed polyphenol known to exert anti-inflammatory and anti-oxidant effects, on high-fat diet (HFD)-induced NAFLD in C57BL/6 J mice and the underlying mechanisms. Four week-old mice were randomly divided into four groups and fed a low-fat diet (LFD), a HFD, a HFD with common rapeseed oil (HFD + CRO) and a HFD with sinapine in rapeseed oil (HFD + SRO) for 12 weeks. Supplementation with sinapine reduced the body weight of HFD mice by 10.99%, and decreased the levels of TG and LDL-C by 15.67% and 73.62%, respectively. In addition, sinapine also suppressed the intestinal NF-κB and TNF-α expressions and enhanced the adipose tissue IRS-1 expression in the HFD mice (P < 0.05). In terms of effects on the gut microbiota, sinapine induced a decrease in the ratio of Firmicutes to Bacteroidetes and increased the abundance of probiotics, such as Lactobacillaceae, Akkermansiaceae and Blautia, along with metabolite short-chain fatty acid (SCFA)-mediated upregulation of G protein-coupled receptor 43 (GPR43) to inhibit expression of inflammatory factors. Our collective results strongly supported the fact that the utility of sinapine as a prebiotic agent could prevent gut dysbiosis and obesity-related chronic diseases, such as insulin resistance (IR) and NAFLD.

Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology

Microbiology has been largely developed thanks to the discovery and optimization of culture media. The first liquid artificial culture medium was created by Louis Pasteur in 1860. Previously, bacterial growth on daily materials such as some foods had been observed. These observations highlighted the importance of the bacteria's natural environment and their nutritional needs in the development of culture media for their isolation. A culture medium is essentially composed of basic elements (water, nutrients), to which must be added different growth factors that will be specific to each bacterium and necessary for their growth. The evolution of bacterial culture through the media used for their culture began with the development of the first solid culture medium by Koch, allowing not only the production of bacterial colonies, but also the possibility of purifying a bacterial clone. The main gelling agent used in solid culture media is agar. However, some limits have been observed in the use of agar because of some extremely oxygen-sensitive bacteria that do not grow on agar media, and other alternatives were proposed and tested. Then, the discovery of antimicrobial agents and their specific targets prompted the emergence of selective media. These inhibiting agents make it possible to eliminate undesirable bacteria from the microbiota and select the bacteria desired. Thanks to a better knowledge of the bacterial environment, it will be possible to develop new culture media and new culture conditions, better adapted to certain fastidious bacteria that are difficult to isolate.

Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors

The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes.IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.

Translating the gut microbiome: ready for the clinic?

Research into the gut microbiota and its role in health and disease has expanded rapidly in the past two decades. However, much of the early focus has been on cataloguing the microorganisms present, identifying correlations between microbial species and disease and using preclinical animal models to understand phenotypes. Now efforts are under way to provide functional insights into the gut microbiota and its mechanisms of action, improve understanding of the role of the microbiota beyond the gut and advance the development of microbiota-based therapeutics so that the microbiome can be harnessed in the clinic. In this Viewpoint article, we asked a selection of scientists and clinicians working in the gut microbiome field for their opinions on the major advances in and the challenges and solutions for translating gut microbiome research to the clinic, and where they expect progress to be made in the future.