Role of the microbiome in human development

Effects of oral exposure to leachate from boiled-water treated plastic products on gut microbiome and metabolomics

By simulating plastic exposure patterns in modern society, the impact of daily exposure to plastic products on mammals was explored. In this study, Institute for Cancer Research (ICR) mice were used to establish drinking water exposure models of three popular kinds of plastic products, including non-woven tea bags, food-grade plastic bags and disposable paper cups. Feces and urine of mice were collected for gut microbiome and metabolomics analysis. Our results showed that the diversity and composition of gut microbiota changed at genus level compared to control group. Lactobacillus, Parabacteroides, Escherichia-shigella and Staphylococcus decreased while Lachnospiraceae increased treated with non-woven tea bags. Escherichia-shigella and Alistipes increased while Parabacteroides decreased treated with food grade plastic bags. Muribaculaceae decreased in the gut microbiota of mice treated with disposable paper cups. Metabolomics has seen changes in the number of metabolites and enrichment of metabolic pathways related to inflammatory responses and immune function. Inflammatory responses were found in histological and biochemical examination. In summary, this study demonstrated that long-term oral exposure to leachate form boiled-water treated plastic products might have effects on gut microbiome and metabolome, which further provided new insights about potential adverse effects for human beings.

microbioTA: an atlas of the microbiome in multiple disease tissues of Homo sapiens and Mus musculus

microbioTA (http://bio-annotation.cn/microbiota) was constructed to provide a comprehensive, user-friendly resource for the application of microbiome data from diseased tissues, helping users improve their general knowledge and deep understanding of tissue-derived microbes. Various microbes have been found to colonize cancer tissues and play important roles in cancer diagnoses and outcomes, with many studies focusing on developing better cancer-related microbiome data. However, there are currently no independent, comprehensive open resources cataloguing cancer-related microbiome data, which limits the exploration of the relationship between these microbes and cancer progression. Given this, we propose a new strategy to re-align the existing next-generation sequencing data to facilitate the mining of hidden sequence data describing the microbiome to maximize available resources. To this end, we collected 417 publicly available datasets from 25 human and 14 mouse tissues from the Gene Expression Omnibus database and use these to develop a novel pipeline to re-align microbiome sequences facilitating in-depth analyses designed to reveal the microbial profile of various cancer tissues and their healthy controls. microbioTA is a user-friendly online platform which allows users to browse, search, visualize, and download microbial abundance data from various tissues along with corresponding analysis results, aimimg at providing a reference for cancer-related microbiome research.

Machine learning on the road to unlocking microbiota's potential for boosting immune checkpoint therapy

The intestinal microbiota is a complex and diverse ecological community that fulfills multiple functions and substantially impacts human health. Despite its plasticity, unfavorable conditions can cause perturbations leading to so-called dysbiosis, which have been connected to multiple diseases. Unfortunately, understanding the mechanisms underlying the crosstalk between those microorganisms and their host is proving to be difficult. Traditionally used bioinformatic tools have difficulties to fully exploit big data generated for this purpose by modern high throughput screens. Machine Learning (ML) may be a potential means of solving such problems, but it requires diligent application to allow for drawing valid conclusions. This is especially crucial as gaining insight into the mechanistic basis of microbial impact on human health is highly anticipated in numerous fields of study. This includes oncology, where growing amounts of studies implicate the gut ecosystems in both cancerogenesis and antineoplastic treatment outcomes. Based on these reports and first signs of clinical benefits related to microbiota modulation in human trials, hopes are rising for the development of microbiome-derived diagnostics and therapeutics. In this mini-review, we're inspecting analytical approaches used to uncover the role of gut microbiome in immune checkpoint therapy (ICT) with the use of shotgun metagenomic sequencing (SMS) data.

The potential mechanism of Liu-Wei-Di-Huang Pills in treatment of type 2 diabetic mellitus: from gut microbiota to short-chain fatty acids metabolism

BACKGROUND

Type 2 diabetes mellitus (T2DM) has already become a global pandemic. Recently, reports showed its pathogenesis was closely related to a disorder of gut microbiota. In China, the Liu-Wei-Di-Huang Pills (LWDH) have treated T2DM for thousands of years. However, its therapeutic mechanism associated with gut microbiota is worthy of further study.

AIMS

This study aims to investigate the effects of LWDH on T2DM by regulating gut microbiota and short-chain fatty acids (SCFAs) in Goto-Kakizaki (GK) rats.

METHODS

T2DM models were successfully established based on GK rats and administrated with LWDH. The changes in fasting blood glucose (FBG), oral glucose tolerance test (OGTT), and serum insulin (INS) were determined, and the immunohistochemical (IHC) method was used to test INS expression in pancreas. The 16S-ribosomal DNA (16S rDNA) sequencing analysis assessed gut microbiota structural changes; a gas chromatography-mass spectrometer (GC-MS)-based metabolomics method was adopted to detect SCFA levels. The pathological morphology of jejunum was detected by hematoxylin-eosin (H&E) staining, and the expression of GPR43, GPR41, GLP-1, and GLP-1R was evaluated by qRT-PCR and ELISA, respectively.

RESULTS

We observed that GK rats treated with LWDH: (a) has altered the microbial structure and promoted the abundance of bacteria in Firmicutes, including Lactobacillus, Allobaculum, and Ruminococcus_2, (b) increased SCFAs levels involving acetic acid, propionic acid, and butyric acid and (c) alleviated T2DM and jejunum injuries potentially based on SCFAs-GPR43/41-GLP-1 pathway.

CONCLUSION

LWDH could improve T2DM by regulating gut microbiota and SCFAs, and the therapeutic mechanism might be related to the SCFAs-GPR43/41-GLP-1 pathway.

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards

As rising temperatures threaten biodiversity across the globe, tropical ectotherms are thought to be particularly vulnerable due to their narrow thermal tolerance ranges. Nevertheless, physiology-based models highlighting the vulnerability of tropical organisms rarely consider the contributions of their gut microbiota, even though microbiomes influence numerous host traits, including thermal tolerance. We combined field and lab experiments to understand the response of the slender anole lizard (Anolis apletophallus) gut microbiome to climatic shifts of various magnitude and duration. First, to examine the effects of long-term climate warming in the wild, we transplanted lizards from the mainland Panama to a series of warmer islands in the Panama Canal and compared their gut microbiome compositions after three generations of divergence. Next, we mimicked the effects of a short-term "heat-wave" by using a greenhouse experiment and explored the link between gut microbiome composition and lizard thermal physiology. Finally, we examined variation in gut microbiomes in our mainland population in the years both before and after a naturally occurring drought. Our results suggest that slender anole microbiomes are surprisingly resilient to short-term warming. However, both the taxonomic and predicted functional compositions of the gut microbiome varied by sampling year across all sites, suggesting that the drought may have had a regional effect. We provide evidence that short-term heat waves may not substantially affect the gut microbiota, while more sustained climate anomalies may have effects at broad geographic scales. IMPORTANCE As climate change progresses, it is crucial to understand how animals will respond to shifts in their local environments. One component of this response involves changes in the microbial communities living in and on host organisms. These "microbiomes" can affect many processes that contribute to host health and survival, yet few studies have measured changes in the microbiomes of wild organisms experiencing novel climatic conditions. We examined the effects of shifting climates on the gut microbiome of the slender anole lizard (Anolis apletophallus) by using a combination of field and laboratory studies, including transplants to warm islands in the Panama Canal. We found that slender anole microbiomes remain stable in response to short-term warming but may be sensitive to sustained climate anomalies, such as droughts. We discuss the significance of these findings for a species that is considered highly vulnerable to climate change.

Significance of Gut Microbiota and Short-Chain Fatty Acids in Heart Failure

Heart failure (HF), as the terminal stage of various heart diseases, seriously threatens an individual’s life, health, and quality of life. Emerging evidence has shown that the gut microbiota comprises an important component of human physiology and metabolic homeostasis, and can directly or indirectly affect the metabolic health of the host through metabolites. Upon in-depth study of intestinal microecology, the “gut-heart axis” appears to provide a novel direction for HF research. Thus, this review primarily focuses on the relationship between the gut microbiota and its major metabolites—i.e., short-chain fatty acids (SCFAs)—and HF. It explores the mechanisms underlying HF and its effective treatment by targeting SCFAs to optimize current HF treatment and thus improve the quality of patients’ lives.

Microbiota profile of new-onset celiac disease in children in Saudi Arabia

Background

Intestinal dysbiosis has been reported to be associated with celiac disease (CeD) in Western populations but little is known in other populations who have different dietary lifestyle and genetic background. The purpose of this study was to determine whether a different microbiota profile is associated with CeD in children in Saudi Arabia.

Results

Forty children with CeD, 20 healthy controls, and 19 non-CeD controls were enrolled. The median age at diagnosis was 10.3, 11.3 and 10.6 years in children with CeD, fecal, and mucosal control groups, respectively. Significant differences in microbial composition between children with CeD and controls both at fecal and mucosal level were identified. Fecal samples were more diverse and richer in bacteria as compared with mucosal samples. Proteobacteria were more abundant in duodenal mucosal samples and Firmicutes and Bacteroides were more abundant in stools. The abundance of many taxa was significantly different between children with CeD and non-CeD controls. In mucosal samples, Bifidobacterium angulatum (unadjusted p = 0.006) and Roseburia intestinalis (unadjusted p = 0.031) were examples of most significantly increased species in children with CeD and non-CeD controls, respectively. In fecal samples, there were 169 bacterial species with significantly different abundance between children with CeD and non- CeD controls.

Conclusions

To our knowledge, this is the first report on the microbial profile in a non-Western population of children with new onset CeD. The fact that mucosal and fecal samples were collected from newly diagnosed children with CeD on normal gluten-containing diet suggests strong association between the identified bacteria and CeD. The identification of many unreported bacterial species significantly associated with CeD, indicates the need for further studies from different populations to expand our understanding of the role of bacteria in the pathogenesis of CeD, hopefully leading to the discovery of new adjuvant treatment options.

The complex immunological role of Helicobacter in modulating cancer

The gut microbiota has recently emerged as a unique mechanism of immunotherapeutic resistance or response within certain cancer patients. Certain adherent bacterial species that reside along the epithelial barrier within the gastrointestinal tract have been shown to be the most immunogenic and include several species within the Helicobacteraceae family. The role of these microbes in cancer remains controversial and varies according to species, immune status, and cancer type. Here, we hypothesize that the functional characteristics rather than the bacterial species of Helicobacteraceae dictate the type of immune response with either a benefit or a detriment to overall cancer progression.

Mixed Fungal Biofilms: From Mycobiota to Devices, a New Challenge on Clinical Practice

Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that allow the evaluation of fungal morphology and the identification of the etiologic agent of mycosis. Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that enable the examination of the fungi for further identification of the etiological agent of the mycosis. The isolation of fungi from pure cultures is typically recommended, as when more than one species is identified, the second agent is considered a contaminant. Fungi mostly survive in highly organized communities that provoke changes in phenotypic profile, increase resistance to antifungals and environmental stresses, and facilitate evasion from the immune system. Mixed fungal biofilms (MFB) harbor more than one fungal species, wherein exchange can occur that potentialize the effects of these virulence factors. However, little is known about MFB and their role in infectious processes, particularly in terms of how each species may synergistically contribute to the pathogenesis. Here, we review fungi present in MFB that are commensals of the human body, forming the mycobiota, and how their participation in MFB affects the maintenance of homeostasis. In addition, we discuss how MFB are formed on both biotic and abiotic surfaces, thus being a significant reservoir of microorganisms that have already been associated in infectious processes of high morbidity and mortality.

Gegen Qinlian decoction ameliorates murine colitis by inhibiting the expansion of Enterobacteriaceae through activating PPAR-γ signaling

Ulcerative colitis (UC) is a chronic and relapsing inflammatory disease of the intestine. Dysbiosis, especially the expansion of facultative anaerobic Enterobacteriaceae, maybe the main pathogenesis of UC. Gegen Qinlian decoction (GD), a traditional Chinese medicinal formula chronicled in the Shang Han Lun, is commonly used to treat UC and has shown an excellent effect on inducing disease remission. However, the role of GD in regulating gut microbiota has not been fully clarified. Herein, we investigated the potential effect of GD on inhibiting the expansion of Enterobacteriaceae and further explored the potential mechanism of this action. Our study demonstrated that GD remarkably reduced body weight loss of colitis mice, shortening of colon length, and inflammation of the colon. Peroxisome proliferator-activated receptor-γ (PPAR-γ) signaling was inactivated in colitis colon tissue, and the abundance of Escherichia coli (E. coli, family of Enterobacteriaceae) in colonic contents and the concentration of lipopolysaccharide (LPS) in colonic tissue were significantly upregulated after DSS-treatment. Notably, GD administration can result in the activation of PPAR-γ and inactivation of iNOS, which lead to the reduction of nitrate, the inhibition of E. coli, and less production of LPS. Combined GD with PPAR-γ antagonist, the effect of GD on the treatment of UC was weakened, and effectless in inhibiting the expansion of Enterobacteriaceae. Therefore, GD ameliorates UC by preventing a dysbiotic expansion of potentially pathogenic E. coli by reducing nitrate levels in the lumen through activating PPAR-γ signaling.

Impacts of Gut Microbiota on the Immune System and Fecal Microbiota Transplantation as a Re-Emerging Therapy for Autoimmune Diseases

The enormous and diverse population of microorganisms residing in the digestive tracts of humans and animals influence the development, regulation, and function of the immune system. Recently, the understanding of the association between autoimmune diseases and gut microbiota has been improved due to the innovation of high-throughput sequencing technologies with high resolutions. Several studies have reported perturbation of gut microbiota as one of the factors playing a role in the pathogenesis of many diseases, such as inflammatory bowel disease, recurrent diarrhea due to Clostridioides difficile infections. Restoration of healthy gut microbiota by transferring fecal material from a healthy donor to a sick recipient, called fecal microbiota transplantation (FMT), has resolved or improved symptoms of autoimmune diseases. This (re)emerging therapy was approved for the treatment of drug-resistant recurrent C. difficile infections in 2013 by the U.S. Food and Drug Administration. Numerous human and animal studies have demonstrated FMT has the potential as the next generation therapy to control autoimmune and other health problems. Alas, this new therapeutic method has limitations, including the risk of transferring antibiotic-resistant pathogens or transmission of genes from donors to recipients and/or exacerbating the conditions in some patients. Therefore, continued research is needed to elucidate the mechanisms by which gut microbiota is involved in the pathogenesis of autoimmune diseases and to improve the efficacy and optimize the preparation of FMT for different disease conditions, and to tailor FMT to meet the needs in both humans and animals. The prospect of FMT therapy includes shifting from the current practice of using the whole fecal materials to the more aesthetic transfer of selective microbial consortia assembled in vitro or using their metabolic products.

Attention-Deficit/Hyperactivity Disorder and the Gut Microbiota–Gut–Brain Axis: Closing Research Gaps through Female Inclusion in Study Design

The gastrointestinal tract harbors a densely populated community of microbes that exhibits sexual dimorphism. Dysbiosis of this community has been associated with chronic human disease states ranging from metabolic diseases to neuropsychiatric disorders (NPDs). The gut microbiota–gut–brain axis (GMGBA) is a bi-directional pathway that facilitates the interaction of the gut microflora with host physiological functions. Recently, research surrounding the potential roles of the GMGBA in the development of NPDs (e.g., depression, anxiety, and autism spectrum disorders (ASDs)) has increased. However, the role of the GMGBA in attention-deficit/hyperactivity disorder (ADHD), an NPD that affects an estimated 8.4% of children (5.1% of female and 11.5% of male children) and 4% of adults (with a male–female odds ratio of 1.6) in the United States, remains understudied. Herein, we synthesize the current literature regarding the GMGBA, ADHD, and the potentially relevant intersections between the GMGBA and ADHD. Recommendations are presented for pathways of future research into the role(s) of the GMGBA in ADHD etiology and symptomatology. Particular focus is given to the potential for the variable of host sex to act as an outcome modifier of the relationship between the GMGBA and ADHD.

Preoperative Intestinal Microbiome and Metabolome in Elderly Patients with Delayed Neurocognitive Recovery

BACKGROUND

Delayed neurocognitive recovery (dNCR) is a common complication of the central nervous system in elderly patients. Currently, it is not clear whether the occurrence of dNCR is associated with the intestinal microbiota and its related metabolites. This study investigated the preoperative intestinal microflora and faecal metabolites of dNCR patients.

METHODS

Twenty-two elderly urological patients were divided into a dNCR group (D group) and a non-dNCR group (ND group) according to the postoperative Mini-Mental State Examination (MMSE) score on the first and third day after surgery. A postoperative MMSE score ≤ 2 points compared with the preoperative score was considered evidence of dNCR. We used a comprehensive method that combined 16S rRNA gene sequencing and untargeted metabolomics to study the preoperative intestinal microflora and faecal metabolites of the two groups, and conducted correlation analysis between them.

RESULTS

Compared with the D group, the microbial community in the ND group was more abundant. At the family level, the ND group was significantly enriched in Lachnospiraceae, Peptostreptococcaceae and Muribaculaceae. At the genus level, the faecal microbiota of the ND group was differentially enriched in Agathobacter, Dorea, Fusicatenibacter, Coprococcus_2 and Romboutsia while that of the D group was differentially enriched in Anaerofilum. Untargeted metabolomics revealed significant differences in eight different metabolites between the two groups, including ribose, ethanol, leucine, maltose, pentadecanoic acid, malonic acid 1,3,4-dihydroxybenzoic acid and 3-hydroxypalmitic acid. In addition, differential metabolites were associated with the abundance of specific bacteria.

CONCLUSIONS

The occurrence of dNCR may be associated with the intestinal flora and its related metabolite composition of patients before surgery.

Characteristics of oral microbiota in plateau and plain youth‐positive correlations between blood lipid level, metabolism and specific microflora in the plateau group

Objectives

To analyze the characteristics of oral microbiota in plateau and plain youth and the possible function of the microbiome.

Materials and methods

A total of 120 healthy young males (80 on the plateau, 40 on the plain) completed this cross-sectional study. Oral microflora samples were collected from all participants. The bacterial 16S rDNA was amplified using PCR and sequenced using Illumina MiSeq high-throughput sequencing. The data were analyzed to determine the microbial distribution and community structure of the oral microflora from the two groups. Metastats was used to test differences in relative species abundance between the groups. The correlation between the abundance of specific bacteria and blood indicators was also analyzed.

Results

As demonstrated by alpha and beta diversity, the plateau group had lower microbial richness and a less even distribution of oral microbiota than the plain group. All predominant phyla and genera were qualitatively similar between the two groups, but their relative abundances differed. The relative abundance of bacteria in the phylum Firmicutes was significantly higher in the plateau group than in the plain group. At the genus level, Streptococcus spp. and Gemella spp. were also more abundant in the plateau group. The functional prediction indicated vigorous microbial metabolism in the oral bacterial community. We also found that the relative abundance of Streptococcus spp., the dominant genus, was positively correlated with triglyceride levels in the plateau group.

Conclusions

With increasing altitude, the diversity of oral microbiota and the relative proportion of predominant bacteria were altered. The distribution and related function of Streptococcus spp. were prominent in plateau samples. This comprehensive study of the relationship between oral microecology and elevation provides a point of reference for studying the human body’s adaptability or inadaptability to high altitude.

A framework for testing the impact of co-infections on host gut microbiomes

Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or more co-infections and their collective impact is largely unexplored. Here we developed a framework illustrating changes to the host gut microbiome following single infections, and build on it by describing the neutral, synergistic or antagonistic impacts on microbial α- and ß-diversity expected from co-infections. We tested the framework on microbiome data from a non-human primate population co-infected with helminths and Adenovirus, and matched patterns reported in published studies to the introduced framework. In this case study, α-diversity of co-infected Malagasy mouse lemurs (Microcebus griseorufus) did not differ in comparison with that of singly infected or uninfected individuals, even though community composition captured with ß-diversity metrices changed significantly. Explicitly, we record stochastic changes in dispersion, a sign of dysbiosis, following the Anna-Karenina principle rather than deterministic shifts in the microbial gut community. From the literature review and our case study, neutral and synergistic impacts emerged as common outcomes from co-infections, wherein both shifts and dispersion of microbial communities following co-infections were often more severe than after a single infection alone, but microbial α-diversity was not universally altered. Important functions of the microbiome may also suffer from such heavily altered, though no less species-rich microbial community. Lastly, we pose the hypothesis that the reshuffling of host-associated microbial communities due to the impact of various, often coinciding parasitic infections may become a source of novel or zoonotic diseases.

Microbiome in cancer: An exploration of carcinogenesis, immune responses and immunotherapy

Cancer is a major disease endangering human health. More and more studies have shown that microorganisms play an extremely important role in the occurrence, development and treatment of tumors. As a very promising tumor treatment strategy, immunotherapy has also been proved to have a great relationship with microorganisms. Here, the authors review the contribution of the microbiota to cancer and the research on its impact on cancer immunotherapy. We also highlight the possible mechanism of their interaction and outlined the potential application of microbiota in tumor immunotherapy.

Longitudinal effects of growth restriction on the murine gut microbiome and metabolome

Undernutrition-induced growth restriction in the early stages of life increases the risk of chronic disease in adulthood. Although metabolic impairments have been observed, few studies have characterized the gut microbiome and gut-liver metabolome profiles of growth-restricted animals during early-to-mid-life development. To induce growth restriction, mouse offspring were either born to gestational undernutrition (GUN) or suckled from postnatal undernutrition (PUN) dams fed a protein-restricted diet (8% protein) or control diet (CON; 20% protein) until weaning at postnatal age of 21 days (PN21). At PN21, all mice were fed the CON diet until adulthood (PN80). Livers were collected at PN21 and PN80, and fecal samples were collected weekly starting at PN21 (postweaning week 1) until PN80 (postweaning week 5) for gut microbiome and metabolome analyses. PUN mice exhibited the most alterations in gut microbiome and gut and liver metabolome compared with CON mice. These mice had altered fecal microbial β-diversity (P = 0.001) and exhibited higher proportions of Bifidobacteriales [linear mixed model (LMM) P = 7.1 × 10^-6), Clostridiales (P = 1.459 × 10^-5), Erysipelotrichales (P = 0.0003), and lower Bacteroidales (P = 4.1 × 10^-5)]. PUN liver and fecal metabolome had a reduced total bile acid pool (P < 0.01), as well as lower abundance of riboflavin (P = 0.003), amino acids [i.e., methionine (P = 0.0018), phenylalanine (P = 0.0015), and tyrosine (P = 0.0041)], and higher excreted total peptides (LMM P = 0.0064) compared with CON. Overall, protein restriction during lactation permanently alters the gut microbiome into adulthood. Although the liver bile acids, amino acids, and acyl-carnitines recovered, the fecal peptides and microbiome remained permanently altered into adulthood, indicating that inadequate protein intake in a specific time frame in early life can have an irreversible impact on the microbiome and fecal metabolome.NEW & NOTEWORTHY Undernutrition-induced early-life growth restriction not only leads to increased disease risk but also permanently alters the gut microbiome and gut-liver metabolome during specific windows of early-life development.

Effects of compound small peptides of Chinese medicine on intestinal immunity and cecal intestinal flora in CTX immunosuppressed mice

The study was designed to explore the improvement effect of CSPCM (compound small peptide of Chinese medicine) on intestinal immunity and microflora through the treatment of different doses of CSPCM. A total of 100 male Kunming mice were weighed and divided into five groups, namely, group A (control group), group B (model group), group C (0.1 g/kg·bw CSPCM), group D (0.2 g/kg·bw CSPCM), and group E (0.4 g/kg·bw CSPCM). The use of CTX (cyclophosphamide) caused a series of negative effects: the secretion of IL-2, IL-22, TNF-α, sIgA, length of the villi, and the area of Pey's node were significantly reduced (P < 0.05); the depth of crypt and the percent of CD3⁺ and CD4⁺ cells were significantly increased (P < 0.05); the cecal flora taxa decreased; the abundance of Firmicutes and Lactobacillus increased; and the abundance of Bacteroidetes, Deferribacteres, Proteobacteria, Mucispirillum, Bacteroides, and Flexisprra decreased. The addition of CSPCM improved the secretion of cytokines and the development of intestinal villi, crypts, and Pey's node. The number of CD3⁺ and CD4⁺ cells in groups C, D, and E was significantly higher than that in group B (P < 0.05). Compared with group B, the abundance of Firmicutes in groups C, D, and E was decreased, and the Bacteroidetes, Deferribacteres, and Proteobacteria increased. The abundance of Lactobacillus decreased, while that of Mucispirillum, Bacteroides, and Flexisprra increased. It is concluded that cyclophosphamide is extremely destructive to the intestinal area and has a great negative impact on the development of the small intestine, the intestinal immune system, and the intestinal flora. The CSPCM can improve the negative effects of CTX.

A complete guide to human microbiomes: Body niches, transmission, development, dysbiosis, and restoration

Humans are supra-organisms co-evolved with microbial communities (Prokaryotic and Eukaryotic), named the microbiome. These microbiomes supply essential ecosystem services that play critical roles in human health. A loss of indigenous microbes through modern lifestyles leads to microbial extinctions, associated with many diseases and epidemics. This narrative review conforms a complete guide to the human holobiont-comprising the host and all its symbiont populations- summarizes the latest and most significant research findings in human microbiome. It pretends to be a comprehensive resource in the field, describing all human body niches and their dominant microbial taxa while discussing common perturbations on microbial homeostasis, impacts of urbanization and restoration and humanitarian efforts to preserve good microbes from extinction.

Mapping trends and hotspot regarding gut microbiota and host immune response: A bibliometric analysis of global research (2011–2021)

Background

Gut microbiota is a complex ecosystem that is vital for the development and function of the immune system, is closely associated with host immunity, and affects human health and disease. Therefore, the current progress and trends in this field must be explored.

Purpose

No bibliometric analysis has been conducted on gut microbiota and host immune response. This study aimed to analyze the current progress and developing trends in this field through bibliometric and visual analysis.

Methods

Global publications on gut microbiota and host immune response from January 2011 to December 2021 were extracted from the Web of Science (WOS) collection database. GraphPad Prism, VOSviewer software, and CiteSpace were employed to perform a bibliometric and visual study.

Results

The number of publications has rapidly increased in the last decade but has declined in the most recent year. The Cooperation network shows that the United States, Harvard Medical School, and Frontiers in Immunology were the most active country, institute, and journal in this field, respectively. Co-occurrence analysis divided all keywords into four clusters: people, animals, cells, and diseases. The latest keyword within all clusters was “COVID,” and the most frequently occurring keyword was “SCFA.”

Conclusion

Gut microbiota and host immune response remain a research hotspot, and their relation to cancer, CNS disorders, and autoimmune disease has been explored. However, additional studies on gut microbiota must be performed, particularly its association with bacterial strain screening and personalized therapy.

Material Engineering in Gut Microbiome and Human Health

Tremendous progress has been made in the past decade regarding our understanding of the gut microbiome's role in human health. Currently, however, a comprehensive and focused review marrying the two distinct fields of gut microbiome and material research is lacking. To bridge the gap, the current paper discusses critical aspects of the rapidly emerging research topic of "material engineering in the gut microbiome and human health." By engaging scientists with diverse backgrounds in biomaterials, gut-microbiome axis, neuroscience, synthetic biology, tissue engineering, and biosensing in a dialogue, our goal is to accelerate the development of research tools for gut microbiome research and the development of therapeutics that target the gut microbiome. For this purpose, state-of-the-art knowledge is presented here on biomaterial technologies that facilitate the study, analysis, and manipulation of the gut microbiome, including intestinal organoids, gut-on-chip models, hydrogels for spatial mapping of gut microbiome compositions, microbiome biosensors, and oral bacteria delivery systems. In addition, a discussion is provided regarding the microbiome-gut-brain axis and the critical roles that biomaterials can play to investigate and regulate the axis. Lastly, perspectives are provided regarding future directions on how to develop and use novel biomaterials in gut microbiome research, as well as essential regulatory rules in clinical translation. In this way, we hope to inspire research into future biomaterial technologies to advance gut microbiome research and gut microbiome-based theragnostics.

Microbial communities in developmental stages of lucinid bivalves

Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host's reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development.

Nutrition and Immunity in Perinatal Hypoxic-Ischemic Injury

Perinatal hypoxia ischaemia (PHI), acute and chronic, may be associated with considerable adverse outcomes in the foetus and neonate. The molecular and cellular mechanisms of injury and repair associated with PHI in the perinate are not completely understood. Increasing evidence is mounting for the role of nutrients and bioactive food components in immune development, function and repair in PHI. In this review, we explore current concepts around the neonatal immune response to PHI with a specific emphasis on the impact of nutrition in the mother, foetus and neonate.

Neonatal immune challenge influences the microbiota and behaviour in a sexually dimorphic manner

There is comorbidity between anxiety disorders and gastrointestinal disorders, with both linked to adverse early life events. The microbiome gut-brain-axis, a bidirectional communication system, is plastic throughout the neonatal period and is a possible mediator of this relationship. Here, we used a well-established neonatal rodent immune activation model to investigate the long-term effect of neonatal lipopolysaccharide (LPS) exposure on adult behaviour and the relationship to microbiome composition. Wistar rats were injected with LPS (0.05 mg/kg) or saline (equivolume) on postnatal days 3 and 5. In adulthood, behavioural tests were performed to assess anxiety-like behaviour, and microbiota sequencing was performed on stool samples. There were distinctly different behavioural phenotypes for LPS-exposed males and females. LPS-exposed males displayed typical anxiety-like behaviours with significantly decreased social interaction (F_(1,22) = 7.576, p = 0.009) and increased defecation relative to saline controls (F_(1,23) = 8.623, p = 0.005). LPS-exposed females displayed a different behavioural phenotype with significantly increased social interaction (F_(1,22) = 6.094, p = 0.018), and exploration (F_(1,24) = 6.359, p = 0.015), compared to saline controls. With respect to microbiota profiling data, Bacteroidota was significantly increased for LPS-exposed females (F_(1,14) = 4.931p = 0.035) and Proteobacteria was decreased for LPS-exposed rats of both sexes versus controls (F_(1,30) = 4.923p = 0.035). Furthermore, alterations in predicted functional pathways for neurotransmitters in faeces were observed with a decrease in the relative abundance of D-glutamine and D-glutamate metabolism in LPS exposed females compared to control females (p < 0.05). This suggests that neonatal immune activation alters both later life behaviour and adult gut microbiota in sex-specific ways. These findings highlight the importance of sex in determining the impact of neonatal immune activation on social behaviour and the gut microbiota.

Impact of the Gastrointestinal Tract Microbiota on Cardiovascular Health and Pathophysiology

The microbiota of the gastrointestinal tract (GIT) is an extremely diverse community of microorganisms, and their collective genomes (microbiome) provide a vast arsenal of biological activities, particularly enzymatic ones, which are far from being fully elucidated. The study of the microbiota (and the microbiome) is receiving great interest from the biomedical community because it carries the potential to improve risk prediction models, refine primary and secondary prevention efforts, and also design more appropriate and personalized therapies, including pharmacological ones. A growing body of evidence, although sometimes impaired by the limited number of subjects involved in the studies, suggests that GIT dysbiosis, that is, the altered microbial composition, has an important role in causing and/or worsening cardiovascular disease (CVD). Bacterial translocation and the alteration of levels of microbe-derived metabolites can thus be important to monitor and modulate because they may lead to initiation and progression of CVD and to its establishment as chronic state. We hereby aim to provide readers with details on available resources and experimental approaches that are used in this fascinating field of biomedical research and on some novelties on the impact of GIT microbiota on CVD.

Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China

The objective of this study was to describe and compare the dynamic microbiota characteristics in the gastrointestinal (GI) tract in Chinese participants via high-throughput sequencing techniques. The study collected saliva, esophageal swab, cardia biopsy, noncardia biopsy, gastric juice, and fecal specimens from 40 participants who underwent upper GI tract cancer screening in Linzhou (Henan, China) in August 2019. The V4 region of 16S rRNA genes was amplified and sequenced using the Illumina MiniSeq platform. The observed amplicon sequence variants (ASVs) gradually decreased from saliva to esophageal swab, cardia biopsy, noncardia biopsy, and gastric juice specimens and then increased from gastric juice to fecal specimens (P < 0.05). Each GI site had its own microbial characteristics that overlapped those of adjacent sites. Characteristic genera for each site were as follows: Neisseria and Prevotella in saliva, Streptococcus and Haemophilus in the esophagus, Helicobacter in the noncardia, Pseudomonas in gastric juice, Faecalibacterium, Roseburia, and Blautia in feces, and Weissella in the cardia. Helicobacter pylori-positive participants had decreased observed ASVs (cardia, P < 0.01; noncardia, P < 0.001) and Shannon index values (cardia, P < 0.001; noncardia, P < 0.001) compared with H. pylori-negative participants both in cardia and noncardia specimens. H. pylori infection played a more important role in the microbial composition of noncardia than of cardia specimens. In gastric juice, the gastric pH and H. pylori infection had similar additive effects on the microbial diversity and composition. These results show that each GI site has its own microbial characteristics that overlap those of adjacent sites and that differences and commonalities between and within microbial compositions coexist, providing essential foundations for the continuing exploration of disease-associated microbiota. IMPORTANCE Upper gastrointestinal (UGI) tract cancer is one of the most common cancers worldwide, while limited attention has been paid to the UGI microbiota. Microbial biomarkers, such as Fusobacteria nucleatum and Helicobacter pylori, bring new ideas for early detection of UGI tract cancer, which may be a highly feasible method to reduce its disease burden. This study revealed that each gastrointestinal site had its own microbial characteristics that overlapped those of adjacent sites. There were significant differences between the microbial compositions of the UGI sites and feces. Helicobacter pylori played a more significant role in the microbial composition of the noncardia stomach than in that of the cardia. Gastric pH and Helicobacter pylori had similar additive effects on the microbial diversity of gastric juice. These findings played a key role in delineating the microbiology spectrum of the gastrointestinal tract and provided baseline information for future microbial exploration covering etiology, primary screening, treatment, outcome, and health care products.

Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions

In mammals, the introduction of solid food is pivotal for the establishment of the gut microbiota. However, the effects of the first food consumed on long-term microbiota trajectory and host response are still largely unknown. This study aimed to investigate the influences of (i) the timing of first solid food ingestion and (ii) the consumption of plant polysaccharides on bacterial community dynamics and host physiology using a rabbit model. To modulate the first exposure to solid nutrients, solid food was provided to suckling rabbits from two different time points (3 or 15 days of age). In parallel, food type was modulated with the provision of diets differing in carbohydrate content throughout life: the food either was formulated with a high proportion of rapidly fermentable fibers (RFF) or was starch-enriched. We found that access to solid food as of 3 days of age accelerated the gut microbiota maturation. Our data revealed differential effects according to the digestive segment: precocious solid food ingestion influenced to a greater extent the development of bacterial communities of the appendix vermiformis, whereas life course polysaccharides ingestion had marked effects on the cecal microbiota. Greater ingestion of RFF was assumed to promote pectin degradation as revealed by metabolomics analysis. However, transcriptomic and phenotypic host responses remained moderately affected by experimental treatments, suggesting little outcomes of the observed microbiome modulations on healthy subjects. In conclusion, our work highlighted the timing of solid food introduction and plant polysaccharides ingestion as two different tools to modulate microbiota implantation and functionality.

IMPORTANCE Our study was designed to gain a better understanding of how different feeding patterns affect the dynamics of gut microbiomes and microbe–host interactions. This research showed that the timing of solid food introduction is a key component of the gut microbiota shaping in early developmental stages, though with lower impact on settled gut microbiota profiles in older individuals. This study also provided in-depth analysis of dietary polysaccharide effects on intestinal microbiota. The type of plant polysaccharides reaching the gut through the lifetime was described as an important modulator of the cecal microbiome and its activity. These findings will contribute to better define the interventions that can be employed for modulating the ecological succession of young mammal gut microbiota.

Gut Microbiota Composition and Diversity in Different Commercial Swine Breeds in Early and Finishing Growth Stages

The gut microbiota affects the metabolism, health and growth rate of pigs. Understanding the characteristics of gut microbiota of different pig breeds at each growth stage will enable the design of individualized feeding strategies. The present study aimed to compare the growth curves and development patterns of pigs of three different breeds (Duroc, Landrace and Yorkshire) using the mathematical models Gompertz, Logistic, Von Bertalanffy and Richards. For Duroc pigs, the Gompertz model showed the highest prediction accuracy (R2 = 0.9974). In contrast, the best models for Landrace and Yorkshire pigs were Richards (R2 = 0.9986) and Von Bertalanffy (R2 = 0.9977), respectively. Path analysis showed that body length (path coefficient  =  0.507) and chest circumference (path coefficient  =  0.532) contributed more significantly to the body weight of pigs at the early growth stage, while hip circumference (path coefficient  =  0.312) had a greater influence on pig body weight in the late growth stage. Moreover, the composition of the gut microbiota of pigs at two growth stages (60 kg of body weight in the early growth stage and 120 kg in the finishing stage) was studied using 16S rRNA sequencing technology. Variations in gut microbiota composition of pigs at different growth stages were observed. KEGG pathway enrichment analysis of annotated metagenomes revealed that protein synthesis and amino acid metabolism pathways were significantly enriched in pigs at the early growth stage, which may be related to nutritional requirements of pigs during this stage. This study confirmed longitudinal variation in the gut microbiota of pigs pertaining to age as well as lateral variation related to pig breed. The present findings expand the current understanding of the variations in swine gut microbiota during production stages.

Endotoxin Biomarkers Are Associated With Adiposity and Cardiometabolic Risk Across 6 Years of Follow-up in Youth

CONTEXT

Metabolic endotoxemia may be a shared mechanism underlying childhood obesity and early-onset metabolic diseases (eg, type 2 diabetes, nonalcoholic fatty liver disease).

OBJECTIVE

Examine prospective associations of serum endotoxin biomarkers lipopolysaccharide (LPS) and its binding protein, LPS binding protein (LBP), and anti-endotoxin core immunoglobulin G (EndoCab IgG) with adiposity and cardiometabolic risk in youth.

DESIGN/SETTING

This prospective study included 393 youth in the Exploring Perinatal Outcomes Among Children cohort in Colorado. Participants were recruited from 2006 to 2009 at age 10 years (baseline) and followed for 6 years (follow-up). We examined associations of endotoxin biomarkers at baseline with adiposity [body mass index (BMI) z-score, visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), skinfolds, waist circumference] and cardiometabolic risk (insulin, glucose, adipokines, lipid profile, blood pressure) across both visits using mixed-effects regression, and with hepatic fat fraction (HFF) at follow-up using linear regression.

RESULTS

Higher LPS and LBP predicted greater adiposity across follow-up. Each 1-unit log-transformed LPS corresponded with 0.23 (95% CI 0.03, 0.43) units BMI z-score, 5.66 (95% CI 1.99, 9.33) mm3 VAT, 30.7 (95% CI 8.0, 53.3) mm3 SAT, and 8.26 (95% CI 4.13, 12.40) mm skinfold sum. EndoCab IgG was associated with VAT only [3.03 (95% CI 0.34, 5.71) mm3]. LPS was associated with higher insulin [1.93 (95% CI 0.08, 3.70) µU/mL] and leptin [2.28 (95% CI 0.66, 3.90) ng/mL] and an adverse lipid profile. No association was observed with HFF. Accounting for pubertal status and lifestyle behaviors did not change findings. However, adjustment for prepregnancy BMI and gestational diabetes attenuated most associations.

CONCLUSIONS

Serum endotoxin may be a marker of pathophysiological processes underlying development of childhood obesity and cardiometabolic conditions associated with exposure to fetal overnutrition.

The Complex Link and Disease Between the Gut Microbiome and the Immune System in Infants

The human gut microbiome is important for human health. The development of stable microbial communities in the gastrointestinal tract is closely related to the early growth and development of host immunity. After the birth of a baby, immune cells and the gut microbiome mature in parallel to adapt to the complex gut environment. The gut microbiome is closely linked to the immune system and influences each other. This interaction is associated with various diseases in infants and young children, such as asthma, food allergies, necrotizing colitis, obesity, and inflammatory bowel disease. Thus, the composition of the infant gut microbiome can predict the risk of disease development and progression. At the same time, the composition of the infant gut microbiome can be regulated in many ways and can be used to prevent and treat disease in infants by modulating the composition of the infant gut microbiome. The most important impacts on infant gut microbiota are maternal, including food delivery and feeding. The differences in the gut microbiota of infants reflect the maternal gut microbiota, which in turn reflects the gut microbiota of a given population, which is clinically significant.

Oral immunization of recombinant Saccharomyces cerevisiae expressing fiber-2 of fowl adenovirus serotype 4 induces protective immunity against homologous infection

Hydropericardium-hepatitis syndrome (HHS) caused by fowl adenovirus (FAdV) serotype 4 strains is a highly contagious disease that causes significant economic loss to the global poultry industry. However, subunit vaccine against FAdV-4 infection is not yet commercially available to date. This study aims to explore the potential for oral immunization of recombinant Saccharomyces cerevisiae expressing Fiber-2 of FAdV-4 as a subunit vaccine. Here, we constructed recombinant S. cerevisiae (ST1814G/Fiber-2) expressing recombinant Fiber-2 (rFiber-2), which was displayed on the cell surface. To evaluate the immune response and protective effect of live recombinant S. cerevisiae, chickens were orally immunized with the constructed live ST1814G/Fiber-2, three times at 5-day intervals, and then challenged with FAdV-4. The results showed that oral administration of live ST1814G/Fiber-2 could stimulate the production of humoral immunity, enhance the body's antiviral activity and immune regulation ability, improve the composition of gut microbiota, provide protection against FAdV-4 challenge, reduce viral load in the liver, and alleviate the pathological damage of heart, liver, and spleen for chicken. In addition, we found the synergistic effect in combining the ST1814G/Fiber-2 yeast and inactivated vaccine to trigger stronger humoral immunity and mucosal immunity. Our results suggest that oral live ST1814G/Fiber-2 is a potentially safer auxiliary preparation strategy in controlling FAdV-4 infection.

Rethinking healthy eating in light of the gut microbiome

Given the worldwide epidemic of diet-related chronic diseases, evidence-based dietary recommendations are fundamentally important for health promotion. Despite the importance of the human gut microbiota for the physiological effects of diet and chronic disease etiology, national dietary guidelines around the world are just beginning to capitalize on scientific breakthroughs in the microbiome field. In this review, we discuss contemporary nutritional recommendations from a microbiome science perspective, focusing on mechanistic evidence that established host-microbe interactions as mediators of the physiological effects of diet. We apply this knowledge to inform discussions of nutrition controversies, advance innovative dietary strategies, and propose an experimental framework that integrates the microbiome into nutrition research. The congruence of key paradigms in the nutrition and microbiome disciplines validates current recommendations in dietary guidelines, and the systematic incorporation of microbiome science into nutrition research has the potential to further improve and innovate healthy eating.

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities

Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.

Fecal Stream Diversion Changes Intestinal Environment, Modulates Mucosal Barrier, and Attenuates Inflammatory Cells in Crohn's Disease

BACKGROUND

The intestinal environment plays important roles in mucosal barrier homeostasis and intestinal inflammation, as clarified in studies using experimental animals but not in humans.

AIMS

We investigated whether environmental changes in the fecal stream cause phenotypic changes in the human mucosal barrier.

METHODS

We obtained human ileal samples after fecal stream diversions in patients with rectal cancer or Crohn's disease. We investigated the bacterial load and diversity in the human defunctioned ileum, defined as the anal side of the ileum relative to the ileostomy. We also examined the epithelium and lamina propria cell phenotypes in the defunctioned ileum.

RESULTS

After fecal stream diversion, bacterial loads decreased significantly in the defunctioned ileum. Based on the Chao1, Shannon, and observed species indices, the diversity of mucosa-associated microbiota was lower in the defunctioned ileum than in the functional ileum. Moreover, the healthy defunctioned ileum showed reductions in villous height, goblet cell numbers, and Ki-67+ cell numbers. Additionally, interferon-γ+, interleukin-17+, and immunoglobulin A+ cell abundance in the lamina propria decreased. After the intestinal environment was restored with an ileostomy closure, the impaired ileal homeostasis recovered. The defunctioned ileum samples from patients with Crohn's disease also showed reductions in interferon-γ+ and interleukin-17+ cell numbers.

CONCLUSIONS

Fecal stream diversion reduced the abundance and diversity of intestinal bacteria. It also altered the intestinal mucosal barrier, similar to the alterations observed in germ-free animals. In patients with Crohn's disease, Th1 and Th17 cell numbers were attenuated, which suggests that the host-microbiome interaction is important in disease pathogenesis.

Role of the Microbiota in Lung Cancer: Insights on Prevention and Treatment

The microbiota is increasingly recognized as a critical player in cancer onset and progression and response to cancer chemotherapy treatment. In recent years, several preclinical and clinical studies have evidenced the involvement of microbiota in lung cancer, one of the world’s deadliest cancers. However, the mechanisms by which the microbiota can impact this type of cancer and patient survival and response to treatments remain poorly investigated. In this review, the peculiarities of the gut and lung microbial ecosystems have been highlighted, and recent findings illustrating the possible mechanisms underlying the microbiota–lung cancer interaction and the host immune response have been discussed. In addition, the mucosal immune system has been identified as a crucial communication frame to ease interactive dynamics between the immune system and the microbiota. Finally, the use of specific next-generation intestinal probiotic strains in counteracting airway diseases has been evaluated. We believe that restoring homeostasis and the balance of bacterial microflora should become part of the routine of integrated cancer interventions, using probiotics, prebiotics, and postbiotics, and promoting a healthy diet and lifestyle.

Prebiotics as a Tool for the Prevention and Treatment of Obesity and Diabetes: Classification and Ability to Modulate the Gut Microbiota

Diabetes and obesity are metabolic diseases that have become alarming conditions in recent decades. Their rate of increase is becoming a growing concern worldwide. Recent studies have established that the composition and dysfunction of the gut microbiota are associated with the development of diabetes. For this reason, strategies such as the use of prebiotics to improve intestinal microbial structure and function have become popular. Consumption of prebiotics for modulating the gut microbiota results in the production of microbial metabolites such as short-chain fatty acids that play essential roles in reducing blood glucose levels, mitigating insulin resistance, reducing inflammation, and promoting the secretion of glucagon-like peptide 1 in the host, and this accounts for the observed remission of metabolic diseases. Prebiotics can be either naturally extracted from non-digestible carbohydrate materials or synthetically produced. In this review, we discussed current findings on how the gut microbiota and microbial metabolites may influence host metabolism to promote health. We provided evidence from various studies that show the ability of prebiotic consumption to alter gut microbial profile, improve gut microbial metabolism and functions, and improve host physiology to alleviate diabetes and obesity. We conclude among other things that the application of systems biology coupled with bioinformatics could be essential in ascertaining the exact mechanisms behind the prebiotic–gut microbe–host interactions required for diabetes and obesity improvement.

Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes

A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy human guts to show that such robust patterns do exist, albeit not in the conventional enterotype sense. We first introduce the concept of mixed-membership enterotypes using a network inference approach based on stochastic block models. We find that gut microbiomes across a group of people (hosts) display a nested structure, which has been observed in a number of ecological systems. This finding led us to designate distinct ecological roles to both microbes and hosts: generalists and specialists. Specifically, generalist hosts have microbiomes with most microbial species, while specialist hosts only have generalist microbes. Moreover, specialist microbes are only present in generalist hosts. From the nested structure of microbial taxonomies, we show that these ecological roles of microbes are generally conserved across datasets. Our results show that the taxonomic composition of healthy human gut microbiomes is associated with robustly structured combinations of generalist and specialist species.

Fecal microbiota monitoring in elite soccer players along the 2019-2020 competitive season

Physical exercise affects the human gut microbiota that, in turn, influences athletes' performance. The current understanding of how the microbiota of professional athletes changes along with different phases of training is sparse. We aim to characterize the fecal microbiota in elite soccer players along with different phases of a competitive season using 16S rRNA gene sequencing. Fecal samples were collected after the summer off-season period, the pre-season retreat, the first half of the competitive season, and the 8 weeks COVID-19 lockdown that interrupted the season 2019-2020. According to our results, the gut microbiota of professional athletes changes along with the phases of the season, characterized by different training, diet, nutritional surveillance, and environment sharing. Pre-season retreat, during which nutritional surveillance and exercise intensity were at their peak, caused a decrease in bacterial groups related to unhealthy lifestyle and an increase in health-promoting symbionts. The competitive season and forced interruption affected other features of the athletes' microbiota, i.e. bacterial groups that respond to dietary fibers load and stress levels. Our longitudinal study, focusing on one of the most followed sports worldwide, provides baseline data for future comparisons and microbiome-targeting interventions aimed at developing personalized training and nutrition plans for performances maximization.

Gut Microbiota and Bone Diseases: A Growing Partnership

Gut microbiota is key to human health and disease. Convincing studies have demonstrated that dysbiosis in the commensal gut microbiota is associated with intestinal and extra-intestinal diseases. Recent explorations have significantly contributed to the understanding of the relationship between gut microbiota and bone diseases (osteoporosis, osteoarthritis, rheumatoid arthritis, and bone cancer). Gut microbiota and its metabolites may become associated with the development and progression of bone disorders owing to their critical role in nutrient absorption, immunomodulation, and the gut-brain-bone axis (regulation hormones). In this work, we review the recent developments addressing the effect of gut microbiota modulation on skeletal diseases and explore a feasible preventive approach and therapy for bone diseases.

Glycomacropeptide Safety and Its Effect on Gut Microbiota in Patients with Phenylketonuria: A Pilot Study

Glycomacropeptide (GMP) represents a good alternative protein source in Phenylketonuria (PKU). In a mouse model, it has been suggested to exert a prebiotic role on beneficial gut bacteria. In this study, we performed the 16S rRNA sequencing to evaluate the effect of 6 months of GMP supplementation on the gut microbiota of nine PKU patients, comparing their bacterial composition and clinical parameters before and after the intervention. GMP seems to be safe from both the microbiological and the clinical point of view. Indeed, we did not observe dramatic changes in the gut microbiota but a specific prebiotic effect on the butyrate-producer Agathobacter spp. and, to a lesser extent, of Subdoligranulum. Clinically, GMP intake did not show a significant impact on both metabolic control, as phenylalanine values were kept below the age target and nutritional parameters. On the other hand, an amelioration of calcium phosphate homeostasis was observed, with an increase in plasmatic vitamin D and a decrease in alkaline phosphatase. Our results suggest GMP as a safe alternative in the PKU diet and its possible prebiotic role on specific taxa without causing dramatic changes in the commensal microbiota.

Immunomodulatory activity of a water-soluble polysaccharide extracted from mussel on cyclophosphamide-induced immunosuppressive mice models

This study aimed to investigate the protective effect of mussel polysaccharide (MP) on cyclophosphamide (Cy)-induced intestinal mucosal immunosuppression and microbial dysbiosis in mice. MP was shown to stimulate secretion of cytokines (SIgA, IL-2, IF-γ, IL-4, IL-10) and production of transcription factors (occludin, claudin-1, ZO-1, mucin-2, IL-2, IF-γ, IL-4, IL-10). Key proteins (p-IκB-α, p-p65) of the NF-κB pathway were upregulated after MP administration. SCFAs levels, which were decreased after the Cy treatment, were improved after treatment with MP. Furthermore, 16 S rRNA sequencing data of fecal samples revealed, through α-diversity and β-diversity analysis, that MP improved microbial community diversity and modulate the overall composition of gut microbiota. Taxonomic composition analysis showed that MP increased the abundance of probiotics species (Lactobacillus) and decreased the proportion of pathogenic species (Desulfovibrio). These findings suggested that MP has a potential immunomodulatory activity on the immunosuppressive mice.

Microbiota Transplantation in an Antibiotic-Induced Bacterial Depletion Mouse Model: Reproducible Establishment, Analysis, and Application

The fecal bacteria transplantation (FMT) technique is indispensable when exploring the pathogenesis and potential treatments for microbiota-related diseases. For FMT clinical treatments, there are already systematic guidelines for donor selection, fecal bacterial separation, FMT frequency, and infusion methods. However, only a few studies have demonstrated the use of standardized FMT procedures for animal models used in theoretical research, creating difficulties for many new researchers in this field. In the present paper, we provide a brief overview of FMT and discuss its contribution to the current understanding of disease mechanisms that relate to microbiota. This protocol can be used to generate a commonly used FMT mouse model and provides a literature reference of customizable steps.

Targeting the gut and tumor microbiota in cancer

Microorganisms within the gut and other niches may contribute to carcinogenesis, as well as shaping cancer immunosurveillance and response to immunotherapy. Our understanding of the complex relationship between different host-intrinsic microorganisms, as well as the multifaceted mechanisms by which they influence health and disease, has grown tremendously-hastening development of novel therapeutic strategies that target the microbiota to improve treatment outcomes in cancer. Accordingly, the evaluation of a patient's microbial composition and function and its subsequent targeted modulation represent key elements of future multidisciplinary and precision-medicine approaches. In this Review, we outline the current state of research toward harnessing the microbiome to better prevent and treat cancer.

Smallpox vaccination induces a substantial increase in commensal skin bacteria that promote pathology and influence the host response

Interactions between pathogens, host microbiota and the immune system influence many physiological and pathological processes. In the 20th century, widespread dermal vaccination with vaccinia virus (VACV) led to the eradication of smallpox but how VACV interacts with the microbiota and whether this influences the efficacy of vaccination are largely unknown. Here we report that intradermal vaccination with VACV induces a large increase in the number of commensal bacteria in infected tissue, which enhance recruitment of inflammatory cells, promote tissue damage and influence the host response. Treatment of vaccinated specific-pathogen-free (SPF) mice with antibiotic, or infection of genetically-matched germ-free (GF) animals caused smaller lesions without alteration in virus titre. Tissue damage correlated with enhanced neutrophil and T cell infiltration and levels of pro-inflammatory tissue cytokines and chemokines. One month after vaccination, GF and both groups of SPF mice had equal numbers of VACV-specific CD8+ T cells and were protected from disease induced by VACV challenge, despite lower levels of VACV-neutralising antibodies observed in GF animals. Thus, skin microbiota may provide an adjuvant-like stimulus during vaccination with VACV and influence the host response to vaccination.

Characterization of Changes and Driver Microbes in Gut Microbiota During Healthy Aging Using A Captive Monkey Model

Recent population studies have significantly advanced our understanding of how age shapes the gut microbiota. However, the actual role of age could be inevitably confounded due to the complex and variable environmental factors in human populations. A well-controlled environment is thus necessary to reduce undesirable confounding effects, and recapitulate age-dependent changes in the gut microbiota of healthy primates. Herein we performed 16S rRNA gene sequencing, characterized the age-associated gut microbial profiles from infant to elderly crab-eating macaques reared in captivity, and systemically revealed the lifelong dynamic changes of the primate gut microbiota. While the most significant age-associated taxa were mainly found as commensals such as Faecalibacterium, the abundance of a group of suspicious pathogens such as Helicobacter was exclusively increased in infants, underlining their potential role in host development. Importantly, topology analysis indicated that the network connectivity of gut microbiota was even more age-dependent than taxonomic diversity, and its tremendous decline with age could probably be linked to healthy aging. Moreover, we identified key driver microbes responsible for such age-dependent network changes, which were further linked to altered metabolic functions of lipids, carbohydrates, and amino acids, as well as phenotypes in the microbial community. The current study thus demonstrates the lifelong age-dependent changes and their driver microbes in the primate gut microbiota, and provides new insights into their roles in the development and healthy aging of their hosts.

The Gut Microbiome May Help Address Mental Health Disparities in Hispanics: A Narrative Review

The gut–brain axis is the biological connection between the enteric and the central nervous systems. Given the expansion of the microbial sciences with the new human microbiome field facilitated by the decrease in sequencing costs, we now know more about the role of gut microbiota in human health. In this short review, particular focus is given to the gut–brain axis and its role in psychiatric diseases such as anxiety and depression. Additionally, factors that contribute to changes in the gut–brain axis, including the gut microbiome, nutrition, the host’s genome, and ethnic difference, are highlighted. Emphasis is given to the lack of studies on Hispanic populations, despite the fact this ethnic group has a higher prevalence of anxiety and depression in the US.

The Oral-Microbiome-Brain Axis and Neuropsychiatric Disorders: An Anthropological Perspective

In the 21st century, neuropsychiatric disorders (NPDs) are on the rise, yet the causal mechanisms behind this global epidemic remain poorly understood. A key to these unknowns may lie within the vast communities of bacteria, fungi, and viruses in the body (microbiota), which are intimately linked with health and disease. NPDs were recently shown to be connected to gut microbiota, which can communicate with and influence the brain through the Gut-Brain-Axis (GBA). Parallel studies examining oral microbiota and their connections to the brain also suggest that microbes in the mouth can similarly influence NPD outcomes. However, the mechanisms and pathways that illuminate how oral microbiota and brain communicate in NPDs remain unknown. Here, we review identified mechanisms and pathways that oral microbiota use to engage the brain, and we lay the theoretical foundation for an oral-microbiota-brain axis (OMBA). Specifically, we examine established neuroinflammatory and immune system activation responses that underpin interactions between the oral microbiota and the central nervous system (CNS), detailing four specific mechanisms: (1) microbial and metabolite escape, (2) neuroinflammation, (3) CNS signaling, and (4) response to neurohormones. We then scrutinize why including the OMBA, in addition to the GBA, is critically needed to elucidate specific causal relationships between microbial dysbiosis and observed NPD development and progression. Furthermore, we argue for comprehensive, interdisciplinary approaches that integrate lab-based microbiome research and population-level studies that examine the OMBA to improve NPDs. We specifically identify key anthropological perspectives that integrate sociocultural, epidemiological, genetic, and environmental factors that shape the oral microbiome and its interactions with NPDs. Together, future studies of the OMBA in conjunction with interdisciplinary approaches can be used to identify NPD risks and improve outcomes, as well as develop novel intervention and treatment strategies.

The Maternal-Fetal Gut Microbiota Axis: Physiological Changes, Dietary Influence, and Modulation Possibilities

The prenatal period and the first years of life have a significant impact on the health issues and life quality of an individual. The appropriate development of the immune system and the central nervous system are thought to be major critical determining events. In parallel to these, establishing an early intestinal microbiota community is another important factor for future well-being interfering with prenatal and postnatal developmental processes. This review aims at summarizing the main characteristics of maternal gut microbiota and its possible transmission to the offspring, thereby affecting fetal and/or neonatal development and health. Since maternal dietary factors are potential modulators of the maternal-fetal microbiota axis, we will outline current knowledge on the impact of certain diets, nutritional factors, and nutritional modulators during pregnancy on offspring's microbiota and health.