From hype to hope: The gut microbiota in enteric infectious disease. Cell. 2015;163:1326-1332. [PMID: 26638069 DOI: 10.1016/j.cell.2015.11.032]

4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs

Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.

Evaluation of the Stereochemistry of Staphyloferrin A for Developing Staphylococcus-Specific Targeting Conjugates

Bacteria in the genus Staphylococcus are pathogenic and harmful to humans. Alarmingly, some Staphylococcus, such as methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) have spread worldwide and become notoriously resistant to antibiotics, threatening and concerning public health. Hence, the development of new Staphylococcus-targeting diagnostic and therapeutic agents is urgent. Here, we chose the S. aureus-secreted siderophore staphyloferrin A (SA) as a guiding unit. We developed a series of Staphyloferrin A conjugates (SA conjugates) and showed the specific targeting ability to Staphylococcus bacteria. Furthermore, among the structural factors we evaluated, the stereo-chemistry of the amino acid backbone of SA conjugates is essential to efficiently target Staphylococci. Finally, we demonstrated that fluorescent Staphyloferrin A probes (SA-FL probes) could specifically target Staphylococci in complex bacterial mixtures.

Public health case for microbiome-sparing antibiotics and new opportunities for drug development

Although antibiotics remain a cornerstone of modern medicine, the issues of widespread antibiotic resistance and collateral damage to the microbiome from antibiotic use are driving a need for drug developers to consider more tailored, patient-directed products to avoid antibiotic-induced perturbations of the structure and function of the indigenous microbiota. This perspective summarizes a cascade of microbiome health effects that is initiated by antibiotic-mediated microbiome disruption at an individual level and ultimately leads to infection and transmission of multidrug-resistant pathogens across patient populations. The scientific evidence behind each of the key steps of this cascade is presented. The interruption of this cascade through the use of highly targeted, microbiome-sparing antibiotics aiming to improve health outcomes is discussed. Further, this perspective reflects on some key clinical trial design and reimbursement considerations to be addressed as part of the drug development path.

Interaction between bacterial microbiota and nematode parasite communities in sheep's gastrointestinal tract

The economic impact of gastrointestinal (GI) nematode infections on livestock production is well documented worldwide. Increasing evidence supports the hypothesis that parasite colonization induces significant changes in the GI tract environment and, therefore, in the landscape where the microbiota and parasites occur. Understanding the interactions between bacterial and parasite populations in the digestive tract of livestock may be useful to design parasite control strategies based on microbiota modification. The aims of this work were to investigate the impact of the oxytetracycline-mediated manipulation of the gut microbial community on the composition of GI nematode populations in naturally infected sheep and to explore changes in the GI microbial communities after nematode population treatment with the anthelmintic compound monepantel. Extensive manipulation of the GI microbiota with a therapeutic dose of the long-acting oxytetracycline formulation did not induce significant changes in the GI nematode burden. The gut microbiota of treated animals returned to control levels 17 days after treatment, suggesting strong resilience of the sheep microbial community to antibiotic-mediated microbiota perturbation. A significant decrease of the bacterial Mycoplasmataceae family (Log2FC = -4, Padj = 0.001) and a marked increase of the Methanobacteriaceae family (Log2FC = 2.9, Padj = 0.018) were observed in the abomasum of sheep receiving the monepantel treatment. While a comprehensive evaluation of the interactions among GI mycoplasma, methanobacteria and nematode populations deserves further assessment, the bacteria-nematode population interactions should be included in future control programs in livestock production. Understanding how bacteria and parasites may influence each other in the GI tract environment may substantially contribute to the knowledge of the role of microbiota composition in nematode parasite establishment and the role of the parasites in the microbiota composition.

Dopamine receptor D2 confers colonization resistance via microbial metabolites

The gut microbiome has major roles in modulating host physiology. One such function is colonization resistance, or the ability of the microbial collective to protect the host against enteric pathogens1-3, including enterohaemorrhagic Escherichia coli (EHEC) serotype O157:H7, an attaching and effacing (AE) food-borne pathogen that causes severe gastroenteritis, enterocolitis, bloody diarrhea and acute renal failure4,5 (haemolytic uremic syndrome). Although gut microorganisms can provide colonization resistance by outcompeting some pathogens or modulating host defence provided by the gut barrier and intestinal immune cells6,7, this phenomenon remains poorly understood. Here, we show that activation of the neurotransmitter receptor dopamine receptor D2 (DRD2) in the intestinal epithelium by gut microbial metabolites produced upon dietary supplementation with the essential amino acid L-tryptophan protects the host against Citrobacter rodentium, a mouse AE pathogen that is widely used as a model for EHEC infection8,9. We further find that DRD2 activation by these tryptophan-derived metabolites decreases expression of a host actin regulatory protein involved in C. rodentium and EHEC attachment to the gut epithelium via formation of actin pedestals. Our results reveal a noncanonical colonization resistance pathway against AE pathogens that features an unconventional role for DRD2 outside the nervous system in controlling actin cytoskeletal organization in the gut epithelium. Our findings may inspire prophylactic and therapeutic approaches targeting DRD2 with dietary or pharmacological interventions to improve gut health and treat gastrointestinal infections, which afflict millions globally.

Exploring clues pointing toward the existence of a brain-gut microbiota-hair follicle axis

Proposing the concept of a brain-gut-skin axis has led some researchers to recognize the relationship among brain activity, gut microbiota, and the skin. Hair follicles are skin accessory organs, a previously unnoticed target tissue for classical neurohormones, neurotrophins, and neuropeptides. Some studies have shown a relationship between the central nervous system and hair follicles that an imbalance in the gut bacteria can affect hair follicle density. This review summarizes existing evidence from literature and explores clues supporting a connection linking the brain, gut microbiota, and hair follicles. It amalgamates previously proposed partial concepts into a new, unified concept-the "brain-gut microbiota-hair follicle" axis, -which suggests that modulation of the microbiome via probiotics can have positive effects on hair follicles. This review also explores how preclinical research on hair follicles can propel novel and clinically untapped applications.

Gut microbiota-gonadal axis: the impact of gut microbiota on reproductive functions

The influence of gut microbiota on physiological processes is rapidly gaining attention globally. Despite being under-studied, there are available data demonstrating a gut microbiota-gonadal cross-talk, and the importance of this axis in reproduction. This study reviews the impacts of gut microbiota on reproduction. In addition, the possible mechanisms by which gut microbiota modulates male and female reproduction are presented. Databases, including Embase, Google scholar, Pubmed/Medline, Scopus, and Web of Science, were explored using relevant key words. Findings showed that gut microbiota promotes gonadal functions by modulating the circulating levels of steroid sex hormones, insulin sensitivity, immune system, and gonadal microbiota. Gut microbiota also alters ROS generation and the activation of cytokine accumulation. In conclusion, available data demonstrate the existence of a gut microbiota-gonadal axis, and role of this axis on gonadal functions. However, majority of the data were compelling evidences from animal studies with a great dearth of human data. Therefore, human studies validating the reports of experimental studies using animal models are important.

What we need to know about the germ-free animal models

The gut microbiota (GM), as a forgotten organ, refers to the microbial community that resides in the gastrointestinal tract and plays a critical role in a variety of physiological activities in different body organs. The GM affects its targets through neurological, metabolic, immune, and endocrine pathways. The GM is a dynamic system for which exogenous and endogenous factors have negative or positive effects on its density and composition. Since the mid-twentieth century, laboratory animals are known as the major tools for preclinical research; however, each model has its own limitations. So far, two main models have been used to explore the effects of the GM under normal and abnormal conditions: the isolated germ-free and antibiotic-treated models. Both methods have strengths and weaknesses. In many fields of host-microbe interactions, research on these animal models are known as appropriate experimental subjects that enable investigators to directly assess the role of the microbiota on all features of physiology. These animal models present biological model systems to either study outcomes of the absence of microbes, or to verify the effects of colonization with specific and known microbial species. This paper reviews these current approaches and gives advantages and disadvantages of both models.

Evaluation of penicillin-resistance and probiotic traits in Lactobacillus plantarum during laboratory evolution

The aim of this study was to obtain the Lactobacillus plantarum ATCC14917 with high-level resistance to penicillin and evaluate their probiotic traits using laboratory evolution assay and whole-genome sequencing. In penicillin environment, the minimum inhibitory concentration (MIC) of L. plantarum to penicillin increased from 1 μg/mL to 16 μg/mL and remained stable after the removal of antibiotic pressure, suggesting that the resistance acquisition to penicillin was an irreversible process. Subsequently, change of probiotic characteristics was further evaluated, and the results showed that the acid tolerance, bile tolerance and adhesion ability were significantly declined in the highly resistant strains. Whole-genome sequencing indicated that genes encoding hypothetical protein, LPXTG-motif cell wall anchor domain protein and acetyltransferase were detected in highly resistant L. plantarum, and these genes were still present after the following subculture in the absence of penicillin, suggesting that these three mutants might be the main reason for the development of penicillin resistance. The homology-based analysis of surrounding DNA regions of mutant genes was further performed and indicated that no resistant genes were located on mobile elements in evolved L. plantarum strains, signifying that the spread of antibiotic resistance genes in the gut would not occur for these mutant genes. This study provided a basis for the combined use of highly resistant L. plantarum and penicillin in the treatment of pathogen induced gut diseases.

The gut microbiome as a guidepost for infection risk in liver transplantation

In this issue, Lehmann et al. addresses the high infection risk in liver transplantation by examining the gut microbiome in a patient cohort. By uncovering a predictive role of the microbiome for the clinical course, the study unravels the gut microbiome as a guidepost for infection risk in liver transplantation.

Tracing the evolving dynamics and research hotspots of microbiota and immune microenvironment from the past to the new era

Gut microbiota can regulate many physiological processes within gastrointestinal tract and other distal sites. Dysbiosis may not only influence chronic diseases like the inflammatory bowel disease (IBD), metabolic disease, tumor and its therapeutic efficacy, but also deteriorate acute injuries. This article aims to review the documents in this field and summarize the research hotspots as well as developing processes. Gut microbiota and immune microenvironment-related documents from 1976 to 2022 were obtained from the Web of Science Core Collection database. Bibliometrics was used to assess the core authors and journals, most contributive countries and affiliations together with hotspots in this field and keyword co-occurrence analysis. Data were visualized to help comprehension. Nine hundred and twelve documents about gut microbiota and immune microenvironment were retrieved, and the annual publications increased gradually. The most productive author, country, and affiliation were "Zitvogel L," USA and "UNIV TEXAS MD ANDERSON CANC CTR," respectively. FRONTIERS IN IMMUNOLOGY, CANCERS, and INTERNATIONAL JOURNAL OF MOLECULAR SCIENCE were the periodicals with most publications. Keyword co-occurrence analysis identified three clusters, including gut microbiota, inflammation, and IBD. Combined with the visualized analysis of documents and keyword co-occurrence as well as literature reading, we recognized three key topics of gut microbiota: cancer and therapy; immunity, inflammation and IBD; acute injuries and metabolic diseases. This article revealed researches on gut microbiota and immune microenvironment were growing. More attention should be given to the latest hotspots like gut microbiota, inflammation, IBD, cancer and immunotherapy, acute traumas, and metabolic diseases.IMPORTANCEGut microbiota can regulate many physiological processes within gastrointestinal tract and other distal sites. Dysbiosis may not only influence chronic diseases like inflammatory bowel disease (IBD), metabolic disease, tumor and its therapeutic efficacy, but also deteriorate acute injuries. While the application of bibliometrics in the field of gut microbiota and immune microenvironment still remains blank, which focused more on the regulation of the gut microbiota on the immune microenvironment of different kinds of diseases. Here, we intended to review and summarize the presented documents in gut microbiota and immune microenvironment field by bibliometrics. And we revealed researches on gut microbiota and immune microenvironment were growing. More attention should be given to the latest hotspots like gut microbiota, inflammation, IBD, cancer and immunotherapy, acute traumas, and metabolic diseases.

Dietary High Glycinin Reduces Growth Performance and Impairs Liver and Intestinal Health Status of Orange-Spotted Grouper (Epinephelus coioides)

The aim of the study was to investigate whether the negative effects of dietary glycinin are linked to the structural integrity damage, apoptosis promotion and microbiota alteration in the intestine of orange-spotted grouper (Epinephelus coioides). The basal diet (FM diet) was formulated to contain 48% protein and 11% lipid. Fish meal was replaced by soybean meal (SBM) in FM diets to prepare the SBM diet. Two experimental diets were prepared, containing 4.5% and 10% glycinin in the FM diets (G-4.5 and G-10, respectively). Triplicate groups of 20 fish in each tank (initial weight: 8.01 ± 0.10 g) were fed the four diets across an 8 week growth trial period. Fish fed SBM diets had reduced growth rate, hepatosomatic index, liver total antioxidant capacity and GSH-Px activity, but elevated liver MDA content vs. FM diets. The G-4.5 exhibited maximum growth and the G-10 exhibited a comparable growth with that of the FM diet group. The SBM and G-10 diets down-regulated intestinal tight junction function genes (occludin, claudin-3 and ZO-1) and intestinal apoptosis genes (caspase-3, caspase-8, caspase-9, bcl-2 and bcl-xL), but elevated blood diamine oxidase activity, D-lactic acid and endotoxin contents related to intestinal mucosal permeability, as well as the number of intestinal apoptosis vs FM diets. The intestinal abundance of phylum Proteobacteria and genus Vibrio in SBM diets were higher than those in groups receiving other diets. As for the expression of intestinal inflammatory factor genes, in SBM and G-10 diets vs. FM diets, pro-inflammatory genes (TNF-α, IL-1β and IL-8) were up-regulated, but anti-inflammatory genes (TGF-β1 and IL-10) were down-regulated. The results indicate that dietary 10% glycinin rather than 4.5% glycinin could decrease hepatic antioxidant ability and destroy both the intestinal microbiota profile and morphological integrity through disrupting the tight junction structure of the intestine, increasing intestinal mucosal permeability and apoptosis. These results further trigger intestinal inflammatory reactions and even enteritis, ultimately leading to the poor growth of fish.

The Diversity of Gut Microbiota at Weaning Is Altered in Prolactin Receptor-Null Mice

Maternal milk supports offspring development by providing microbiota, macronutrients, micronutrients, immune factors, and hormones. The hormone prolactin (PRL) is an important milk component with protective effects against metabolic diseases. Because maternal milk regulates microbiota composition and adequate microbiota protect against the development of metabolic diseases, we aimed to investigate whether PRL/PRL receptor signaling regulates gut microbiota composition in newborn mice at weaning. 16SrRNA sequencing of feces and bioinformatics analysis was performed to evaluate gut microbiota in PRL receptor-null mice (Prlr-KO) at weaning (postnatal day 21). The normalized colon and cecal weights were higher and lower, respectively, in the Prlr-KO mice relative to the wild-type mice (Prlr-WT). Relative abundances (Simpson Evenness Index), phylogenetic diversity, and bacterial concentrations were lower in the Prlr-KO mice. Eleven bacteria species out of 470 differed between the Prlr-KO and Prlr-WT mice, with two genera (Anaerotruncus and Lachnospiraceae) related to metabolic disease development being the most common in the Prlr-KO mice. A higher metabolism of terpenoids and polyketides was predicted in the Prlr-KO mice compared to the Prlr-WT mice, and these metabolites had antimicrobial properties and were present in microbe-associated pathogenicity. We concluded that the absence of the PRL receptor altered gut microbiota, resulting in lower abundance and richness, which could contribute to metabolic disease development.

A Moonlighting Protein Secreted by a Nasal Microbiome Fortifies the Innate Host Defense Against Bacterial and Viral Infections

Evidence suggests that the human respiratory tract, as with the gastrointestinal tract, has evolved to its current state in association with commensal microbes. However, little is known about how the airway microbiome affects the development of airway immune system. Here, we uncover a previously unidentified mode of interaction between host airway immunity and a unique strain (AIT01) of Staphylococcus epidermidis, a predominant species of the nasal microbiome. Intranasal administration of AIT01 increased the population of neutrophils and monocytes in mouse lungs. The recruitment of these immune cells resulted in the protection of the murine host against infection by Pseudomonas aeruginosa, a pathogenic bacterium. Interestingly, an AIT01-secreted protein identified as GAPDH, a well-known bacterial moonlighting protein, mediated this protective effect. Intranasal delivery of the purified GAPDH conferred significant resistance against other Gram-negative pathogens (Klebsiella pneumoniae and Acinetobacter baumannii) and influenza A virus. Our findings demonstrate the potential of a native nasal microbe and its secretory protein to enhance innate immune defense against airway infections. These results offer a promising preventive measure, particularly relevant in the context of global pandemics.

Potential role of gut microbes in the efficacy and toxicity of immune checkpoints inhibitors

In recent years, Immune checkpoint inhibitors have been extensively used in the treatment of a variety of cancers. However, the response rates ranging from 13% to 69% depending on the tumor type and the emergence of immune-related adverse events have posed significant challenges for clinical treatment. As a key environmental factor, gut microbes have a variety of important physiological functions such as regulating intestinal nutrient metabolism, promoting intestinal mucosal renewal, and maintaining intestinal mucosal immune activity. A growing number of studies have revealed that gut microbes further influence the anticancer effects of tumor patients through modulation of the efficacy and toxicity of immune checkpoint inhibitors. Currently, faecal microbiota transplantation (FMT) have been developed relatively mature and suggested as an important regulator in order to enhance the efficacy of treatment. This review is dedicated to exploring the impact of differences in flora composition on the efficacy and toxicity of immune checkpoint inhibitors as well as to summarizing the current progress of FMT.

The roles of dietary lipids and lipidomics in gut-brain axis in type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM), one of the main types of Noncommunicable diseases (NCDs), is a systemic inflammatory disease characterized by dysfunctional pancreatic β-cells and/or peripheral insulin resistance, resulting in impaired glucose and lipid metabolism. Genetic, metabolic, multiple lifestyle, and sociodemographic factors are known as related to high T2DM risk. Dietary lipids and lipid metabolism are significant metabolic modulators in T2DM and T2DM-related complications. Besides, accumulated evidence suggests that altered gut microbiota which plays an important role in the metabolic health of the host contributes significantly to T2DM involving impaired or improved glucose and lipid metabolism. At this point, dietary lipids may affect host physiology and health via interaction with the gut microbiota. Besides, increasing evidence in the literature suggests that lipidomics as novel parameters detected with holistic analytical techniques have important roles in the pathogenesis and progression of T2DM, through various mechanisms of action including gut-brain axis modulation. A better understanding of the roles of some nutrients and lipidomics in T2DM through gut microbiota interactions will help develop new strategies for the prevention and treatment of T2DM. However, this issue has not yet been entirely discussed in the literature. The present review provides up-to-date knowledge on the roles of dietary lipids and lipidomics in gut-brain axis in T2DM and some nutritional strategies in T2DM considering lipids- lipidomics and gut microbiota interactions are given.

Dopamine receptor D2 confers colonization resistance via gut microbial metabolites

The gut microbiome plays major roles in modulating host physiology. One such function is colonization resistance, or the ability of the microbial collective to protect the host against enteric pathogens1-3, including enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7, an attaching and effacing (AE) food-borne pathogen that causes severe gastroenteritis, enterocolitis, bloody diarrhea, and acute renal failure (hemolytic uremic syndrome)4,5. Although gut microbes can provide colonization resistance by outcompeting some pathogens or modulating host defense provided by the gut barrier and intestinal immune cells, this phenomenon remains poorly understood. Emerging evidence suggests that small-molecule metabolites produced by the gut microbiota may mediate this process6. Here, we show that tryptophan (Trp)-derived metabolites produced by the gut bacteria protect the host against Citrobacter rodentium, a murine AE pathogen widely used as a model for EHEC infection7,8, by activation of the host neurotransmitter dopamine receptor D2 (DRD2) within the intestinal epithelium. We further find that these Trp metabolites act through DRD2 to decrease expression of a host actin regulatory protein involved in C. rodentium and EHEC attachment to the gut epithelium via formation of actin pedestals. Previously identified mechanisms of colonization resistance either directly affect the pathogen by competitive exclusion or indirectly by modulation of host defense mechanisms9,10, so our results delineate a noncanonical colonization resistance pathway against AE pathogens featuring an unconventional role for DRD2 outside the nervous system in controlling actin cytoskeletal organization within the gut epithelium. Our findings may inspire prophylactic and therapeutic approaches for improving gut health and treating gastrointestinal infections, which afflict millions globally.

Genes mcr improve the intestinal fitness of pathogenic E. coli and balance their lifestyle to commensalism

BACKGROUND

The plasmid-mediated resistance gene mcr-1 confers colistin resistance in Escherichia coli and paves the way for the evolution to pan-drug resistance. We investigated the impact of mcr-1 in gut colonization in the absence of antibiotics using isogenic E. coli strains transformed with a plasmid encoding or devoid of mcr-1.

RESULTS

In gnotobiotic and conventional mice, mcr-1 significantly enhanced intestinal anchoring of E. coli but impaired their lethal effect. This improvement of intestinal fitness was associated with a downregulation of intestinal inflammatory markers and the preservation of intestinal microbiota composition. The mcr-1 gene mediated a cross-resistance to antimicrobial peptides secreted by the microbiota and intestinal epithelial cells (IECs), enhanced E. coli adhesion to IECs, and decreased the proinflammatory activity of both E. coli and its lipopolysaccharides.

CONCLUSION

Overall, mcr-1 changed multiple facets of bacterial behaviour and appeared as a factor enhancing commensal lifestyle and persistence in the gut even in the absence of antibiotics. Video Abstract.

Effects of fecal microbiota transplantation from yaks on weaning diarrhea, fecal microbiota composition, microbial network structure and functional pathways in Chinese Holstein calves

This study was conducted to investigate the effect of fecal microbiota transplantation (FMT) from yaks on weaning diarrhea, fecal microbiota composition, microbial network structure and functional pathways in Chinese Holstein Calves. In this study, 50 calves were randomly divided into five groups of 10 each: NC group (no supplementation), Control group (normal saline), low concentration FMT group (LFMT, 1 × 108 CFU/ml), high concentration FMT group (HMFT, 1 × 109 CFU/ml), and sterilized FMT group (SMFT, sterilized bacterial solution). The test lasted for 30 days. We found that FMT reduced the incidence of diarrhea in weaned calves, and the anti-diarrhea effect of LFMT was stronger than those of HFMT and SFMT. Calf feces were collected by rectal palpation on days 5, 10, 15, and 20 post-weaning, and high-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer region of fecal microbiota was performed. We observed that the richness and diversity of bacterial microbiota in the LFMT, HFMT, and SFMT groups were higher than those in the NC and Control groups at day 20 after weaning. The treatment had a significant effect on bacterial richness (p < 0.05), but not on fungal diversity or richness. The analysis of gut microbiome showed that Firmicutes and Bacteroides were the main bacterial phyla in the feces of weaned calves, and norank_ f Muribaculaceae, UCG-005, Rikenellaceae_RC9_gut_group, Bacteroides, and Blautia were the main genera. Ascomycota and Basidiomycota were the main fungal phyla. Compared to abundance parameters in the Control and NC groups, relative abundances of Firmicutes in the FMT groups increased at different time points after weaning. The relative abundance of Blautia and Lactobacillus in the LFMT group increased significantly after weaning. In addition, abundances of Ruminococcus and Romboutsia, which produce short-chain fatty acids, were also increased in different FMT groups. FMT significantly increased the relative abundance of beneficial bacteria, enhanced the complexity of the fecal microbial network, and promoted important metabolic and cellular processes in weaned calves. In conclusion, our study provides a reference and theoretical basis for FMT to prevent calf weaning diarrhea and other intestinal diseases in ruminants.

Intermittent Parathyroid Hormone Alters Gut Microbiota in Ovariectomized Osteoporotic Rats

Objective

To investigate the effect of intermittent parathyroid hormone (PTH) on gut microbiota (GM) in ovariectomized (OVX) osteoporotic rats.

Methods

Thirty female Sprague–Dawley rats were divided into three groups: sham‐operation (SHAM) group, OVX group and PTH treatment group. After 3 months of treatment, the femurs, serum and feces were acquired for micro‐CT, biochemical analysis and 16S rRNA sequencing, respectively. For 16S rRNA sequencing, after raw reads filtrated and chimera sequences removed, the clean reads were obtained. According to these clean reads, the operational taxonomic units (OTUs) were clustered. Venn diagram analysis was conducted to explore common and unique GM among the three groups. The α‐diversity analysis including Shannon and Simpson indexes were used to evaluate the richness and diversity of the GM. The β‐diversity analysis was performed to estimate the structure of GM. The metabolic function was predicted by Tax4Fun analysis.

Results

With micro‐CT and biochemical analysis, significant improvements were found in the PTH group compared with the OVX group. In Venn diagram analysis, more unique OTUs were found in the SHAM and PTH groups than the OVX group. According to the rank abundance curve, the SHAM and PTH groups had similar richness and evenness, which were higher than the OVX group. Simpson and Shannon indexes were higher in the SHAM and PTH groups compared with the OVX group, indicating that the SHAM and PTH groups had higher microbiota complexity than the OVX group. In β‐diversity analysis, apparent separation was found in the OVX group from the PTH and SHAM groups, which suggested that osteoporosis is the critical factor influencing the GM composition and PTH treatment and can restore the structure of GM. Compared with the OVX group, treatment with PTH increased the abundances of GM which were reported to increase bone mass, such as Lactobacillus_reuteri, Muribaculaceae, Ruminococcaceae, and Clostridia, and inhibited the relative abundance of Rikenellaceae, which was reported to be potentially related to osteoporosis. GM function analysis showed that PTH could promote butyrate synthesis. In Tax4Fun analysis, the function of butanoate metabolism is more vital in the PTH group than the OVX and SHAM groups, suggesting PTH treatment could regulate microbial metabolic function, including butanoate metabolism.

Conclusion

Intermittent PTH can interact with GM through increasing the abundance of probiotics and reducing the abundance of the pathogenic bacteria to enhance the bone mass.

Mapping the global research landscape on nutrition and the gut microbiota: Visualization and bibliometric analysis

BACKGROUND

Nutrition is a significant modifiable element that influences the composition of the gastrointestinal microbiota, implying the possibility of therapeutic diet methods that manipulate the composition and diversity of the microbial.

AIM

To overview research papers on nutrition and gut microbiota and determines the hotspots in this field at the global level.

METHODS

Scopus and Reference Citation Analysis were used to construct a bibliometric technique. It was decided to create bibliometric indicators and mapping as in most previous studies. 2012 through 2021 served as the study's timeframe.

RESULTS

A total of 5378 documents from the Scopus database were selected for analysis. Of all retrieved studies, 78.52% were research papers (n = 4223), followed by reviews (n = 820; 15.25%). China ranked first with a total number of articles of 1634 (30.38%), followed by the United States in second place with a total number of articles of 1307 (24.3%). In the last decade, emerging hotspots for gut microbiota and nutrition research included "gut microbiota metabolism and interaction with dietary components", "connection between the gut microbiota and weight gain", and "the influence of high-fat diet and gut microbiota on metabolic disorders".

CONCLUSION

This is the first thorough bibliometric analysis of nutrition and gut microbiota publications conducted on a global level. Investigation of the association between nutrition/diet and the gut microbiota is still in its infancy and will be expanded in the future. However, according to recent trends, the "effect of gut microbiota and high-fat diet on metabolic disorders" will be an increasing concern in the future.

Comparison of whole goat milk and its major fractions regarding the modulation of gut microbiota

BACKGROUND

Goat milk can be important for human nutrition because of its nutritional value, which may be attributed to its richness in protein, lactose, fat, and other bioactive components. This study compared the diversity and composition of gut microbiota in response to whole goat milk and its major fractions (milk fat, casein, milk whey, whey protein, and whey supernatant). Goat milk, its major fractions, and sterile distilled water (for the control group) were administered to mice intragastrically, and gut microbiota were compared in these groups using metagenomic analysis.

RESULTS

We observed distinct patterns of gut microbiota from different diet groups. The sample distance heatmap showed that, compared with other goat milk fractions, gut microbiota in the casein group was more similar to that in the whole goat-milk group. The relative abundance of the genus Lactobacillus increased significantly after whole goat-milk treatment; the milk whey fraction increased the abundance of Blautia; milk fat and milk whey related fractions treatment promoted the population of Bacteroides. The network analysis showed that genera Lactobacillus and Lactococcus were negatively associated with Helicobacter and Acinetobacter, respectively.

CONCLUSION

Fractions of goat milk could contain different gut microbiota from whole goat milk. Consumption of certain goat milk fractions could increase the ingestion of beneficial bacteria and inhibit the growth of some pathogenic bacteria. Our results could provide the basis for the research into and development of goat-milk based functional foods. © 2021 Society of Chemical Industry.

Riboflavin Attenuates Influenza Virus Through Cytokine-Mediated Effects on the Diversity of the Gut Microbiota in MAIT Cell Deficiency Mice

Influenza is a serious respiratory disease that continues to threaten global health. Mucosa-associated invariant T (MAIT) cells use T-cell receptors (TCRs) that recognize microbial riboflavin derived intermediates presented by the major histocompatibility complex (MHC) class I-like protein MR1. Riboflavin synthesis is broadly conserved, but the roles or mechanisms of riboflavin in MR1^–/– mouse influenza infection are not well understood. In our study, immunofluorescence techniques were applied to analyze the number and distribution of viruses in lung tissue. The amount of cytokine expression was assessed by flow cytometry (FCM), ELISA, and qPCR. The changes in the fecal flora of mice were evaluated based on amplicon sequencing of the 16S V3-V4 region. Our study showed that MAIT cell deficiency increased mortality and that riboflavin altered these effects in microbiota-depleted mice. The oral administration of riboflavin inhibited IL-1β, IL-17A, and IL-18 production but significantly increased the expression of IFN-γ, TNF-α, CCL2, CCL3, and CCL4 in a mouse model. The analysis of the mouse flora revealed that riboflavin treatment significantly increased the relative abundance of Akkermansia and Lactobacillus (p < 0.05) and decreased that of Bacteroides. In contrast, MR1^–/– mice exhibited a concentrated aggregation of Bacteroides (p < 0.01), which indicated that MAIT cell deficiency reduced the diversity of the bacterial population. Our results define the functions of MAIT cells and riboflavin in resistance to influenza virus and suggest a potential role for riboflavin in enhancing MAIT cell immunity and the intestinal flora diversity. Gut populations can be expanded to enhance host resistance to influenza, and the results indicate novel interactions among viruses, MAIT cells, and the gut microbiota.

Enterotoxigenic Escherichia coli: intestinal pathogenesis mechanisms and colonization resistance by gut microbiota

Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and travelers in developing countries. ETEC is characterized by the ability to produce major virulence factors including colonization factors (CFs) and enterotoxins, that bind to specific receptors on epithelial cells and induce diarrhea. The gut microbiota is a stable and sophisticated ecosystem that performs a range of beneficial functions for the host, including protection against pathogen colonization. Understanding the pathogenic mechanisms of ETEC and the interaction between the gut microbiota and ETEC represents not only a research need but also an opportunity and challenge to develop precautions for ETEC infection. Herein, this review focuses on recent discoveries about ETEC etiology, pathogenesis and clinical manifestation, and discusses the colonization resistances mediated by gut microbiota, as well as preventative strategies against ETEC with an aim to provide novel insights that can reduce the adverse effect on human health.

Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement

Recent studies indicate that the human intestinal microbiota could impact the outcome of infection by Vibrio cholerae, the etiological agent of the diarrheal disease cholera. A commensal bacterium, Paracoccus aminovorans, was previously identified in high abundance in stool collected from individuals infected with V. cholerae when compared to stool from uninfected persons. However, if and how P. aminovorans interacts with V. cholerae has not been experimentally determined; moreover, whether any association between this bacterium alters the behaviors of V. cholerae to affect the disease outcome is unclear. Here, we show that P. aminovorans and V. cholerae together form dual-species biofilm structure at the air–liquid interface, with previously uncharacterized novel features. Importantly, the presence of P. aminovorans within the murine small intestine enhances V. cholerae colonization in the same niche that is dependent on the Vibrio exopolysaccharide and other major components of mature V. cholerae biofilm. These studies illustrate that multispecies biofilm formation is a plausible mechanism used by a gut microbe to increase the virulence of the pathogen, and this interaction may alter outcomes in enteric infections.

An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness

Antibiotics are commonly used in the Intensive Care Unit (ICU); however, several studies showed that the impact of antibiotics to prevent infection, multi-organ failure, and death in the ICU is less clear than their benefit on course of infection in the absence of organ dysfunction. We characterized here the compositional and metabolic changes of the gut microbiome induced by critical illness and antibiotics in a cohort of 75 individuals in conjunction with 2,180 gut microbiome samples representing 16 different diseases. We revealed an "infection-vulnerable" gut microbiome environment present only in critically ill treated with antibiotics (ICU⁺). Feeding of Caenorhabditis elegans with Bifidobacterium animalis and Lactobacillus crispatus, species that expanded in ICU⁺ patients, revealed a significant negative impact of these microbes on host viability and developmental homeostasis. These results suggest that antibiotic administration can dramatically impact essential functional activities in the gut related to immune responses more than critical illness itself, which might explain in part untoward effects of antibiotics in the critically ill.

A randomised, double-blind, placebo-controlled trial of Bifidobacterium bifidum CCFM16 for manipulation of the gut microbiota and relief from chronic constipation

A variety of opinions exist on the potential of probiotics to provide relief from chronic constipation with much focus being placed on their mechanism of action and causes of heterogeneity in the results of different studies. We aimed to determine the efficacy and safety of ingesting Bifidobacterium bifidum (B. bifidum) CCFM16 for 28 days to relieve constipation and to understand the mechanism of action. Using Rome IV criterion, 53 and 50 participants diagnosed with chronic constipation were included in the probiotic group and placebo group, respectively. Spontaneous bowel movements (SBMs) per week, stool consistency (Bristol Stool Form Scale [BSFS]), the proportion of SBM responders, patient assessment of constipation symptoms (PAC-SYM), and quality of life (PAC-QoL) were evaluated. The gut microbiota, short-chain fatty acids (SCFAs) and other indicators were also assessed. B. bifidum CCFM16 treatment improved the stool consistency and increased the proportion of SBM responders, but the differences in PAC-SYM and PAC-QoL were statistically insignificant between the groups. Analysis of the SCFAs and microbiome revealed that CCFM16 significantly increased the acetic acid and butyric acid concentrations and enhanced the Firmicutes/Bacteroidetes ratio. Levels of Clostridia were particularly increased and were associated with the increase in butyric acid. In addition, we found the other side of Clostridia; several taxa in the order Clostridiales were observed to prevent CCFM16 from proper functioning in the pre-treatment microbiome. In conclusion, CCFM16 can potentially and efficaciously relieve chronic constipation in Chinese adults by regulating the gut microbiota and SCFA metabolism. The two sides of Clostridia illustrate its importance in microbial therapy for constipation.

The crosstalk between gut microbiota, intestinal immunological niche and visceral adipose tissue as a new model for the pathogenesis of metabolic and inflammatory diseases: the paradigm of type 2 diabetes mellitus

Gut microbiota (GM) comprises more than one thousand microorganisms between bacterial species, viruses, fungi, and protozoa, and represents the main actor of a wide net of molecular interactions, involving, among others, the endocrine system, immune responses, and metabolism. GM influences many endocrine functions such as adrenal steroidogenesis, thyroid function, sexual hormones, IGF-1 pathway and peptides produced in gastrointestinal system. It is fundamental in glycaemic control and obesity, while also exerting an important function in modulating the immune system and associated inflammatory disease. The result of this crosstalk in gut mucosa is the formation of the intestinal immunological niche. Visceral adipose tissue (VAT) produces about 600 different peptides, it is involved in lipid and glucose metabolism and in some immune reactions through several adipokines. GM and VAT interact in a bidirectional fashion: while gut dysbiosis can modify VAT adipokines and hormone secretion, VAT hyperplasia modifies GM composition. Acquired or genetic factors leading to gut dysbiosis or increasing VAT (i.e., Western diet) induce a proinflammatory condition, which plays a pivotal role in the development of dysmetabolic and immunologic conditions, such as diabetes mellitus. Diabetes is clearly associated with specific patterns of GM alterations, with an abundance or reduction of GM species involved in controlling mucosal barrier status, glycaemic levels and exerting a pro- or anti-inflammatory activity. All these factors could explain the higher incidence of several inflammatory conditions in Western countries; furthermore, besides the specific alterations observed in diabetes, this paradigm could represent a common pathway acting in many metabolic conditions and could pave the way to a new, interesting therapeutic approach.

Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

The mammalian gut microbial community, known as the gut microbiota, comprises trillions of bacteria, which co-evolved with the host and has an important role in a variety of host functions that include nutrient acquisition, metabolism, and immunity development, and more importantly, it plays a critical role in the protection of the host from enteric infections associated with exogenous pathogens or indigenous pathobiont outgrowth that may result from healthy gut microbial community disruption. Microbiota evolves complex mechanisms to restrain pathogen growth, which included nutrient competition, competitive metabolic interactions, niche exclusion, and induction of host immune response, which are collectively termed colonization resistance. On the other hand, pathogens have also developed counterstrategies to expand their population and enhance their virulence to cope with the gut microbiota colonization resistance and cause infection. This review summarizes the available literature on the complex relationship occurring between the intestinal microbiota and enteric pathogens, describing how the gut microbiota can mediate colonization resistance against bacterial enteric infections and how bacterial enteropathogens can overcome this resistance as well as how the understanding of this complex interaction can inform future therapies against infectious diseases.

Gut Microbiota: A Potential Target for Cancer Interventions

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

Rumen-protected glucose supplementation in transition dairy cows shifts fermentation patterns and enhances mucosal immunity

Manipulation of perinatal diets, such as supplementing feed with rumen-protected glucose (RPG), has been positively regarded as a strategy to improve milking performance. This study was conducted to assess the effects of RPG on the fermentation profiles, resident microbiota and mucosal immunity in the cecum. Ten Holstein dairy cows were randomly assigned to either a 25 g/kg RPG diet (DM basis) or a 11 g/kg coating fat diet (control, CON). Compared with the CON group, the acetate-to-propionate ratio was lower in the RPG group. Gene expression analysis indicated that RPG supplementation tended to upregulate the expression of Na⁺/H⁺ hydrogen exchanger 3 (NHE3) (P = 0.076). RPG supplementation downregulated the expression of genes involved in self-rehabilitation such as matrix metalloproteinase 1 (MMP1), MMP3, MMP9 and MMP13. Additionally, the mRNA expression of genes involved in immunity including Toll-like receptors (TLR4, TLR6 and TLR7) and proinflammatory cytokines (immune interferon gamma [IFNG] and interleukins interleukin 17A [IL17F], IL17A, IL22), was downregulated by RPG supplementation. Nonetheless, no differences existed in the bacterial copy number and beta diversity between the 2 groups. Overall, supplementation with RPG would probably cause a shift towards propionate production in the cecal digesta, and promote the immune homeostasis of the cecal mucosa in transition dairy cows. Our results extended the basic understanding of RPG supplementation and utilization in transition dairy cows in terms of host microbe interplay in the cecum.

Microbiota-Gut-Brain Axis and Epilepsy: A Review on Mechanisms and Potential Therapeutics

The gut-brain axis refers to the bidirectional communication between the gut and brain, and regulates intestinal homeostasis and the central nervous system via neural networks and neuroendocrine, immune, and inflammatory pathways. The development of sequencing technology has evidenced the key regulatory role of the gut microbiota in several neurological disorders, including Parkinson's disease, Alzheimer's disease, and multiple sclerosis. Epilepsy is a complex disease with multiple risk factors that affect more than 50 million people worldwide; nearly 30% of patients with epilepsy cannot be controlled with drugs. Interestingly, patients with inflammatory bowel disease are more susceptible to epilepsy, and a ketogenic diet is an effective treatment for patients with intractable epilepsy. Based on these clinical facts, the role of the microbiome and the gut-brain axis in epilepsy cannot be ignored. In this review, we discuss the relationship between the gut microbiota and epilepsy, summarize the possible pathogenic mechanisms of epilepsy from the perspective of the microbiota gut-brain axis, and discuss novel therapies targeting the gut microbiota. A better understanding of the role of the microbiota in the gut-brain axis, especially the intestinal one, would help investigate the mechanism, diagnosis, prognosis evaluation, and treatment of intractable epilepsy.

Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections

The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.

Geographic differences in gut microbiota composition impact susceptibility to enteric infection

Large-scale studies of human gut microbiomes have revealed broad differences in composition across geographically distinct populations. Yet, studies examining impacts of microbiome composition on various health outcomes typically focus on single populations, posing the question of whether compositional differences between populations translate into differences in susceptibility. Using germ-free mice humanized with microbiome samples from 30 donors representing three countries, we observe robust differences in susceptibility to Citrobacter rodentium, a model for enteropathogenic Escherichia coli infections, according to geographic origin. We do not see similar responses to Listeria monocytogenes infections. We further find that cohousing the most susceptible and most resistant mice confers protection from C. rodentium infection. This work underscores the importance of increasing global participation in microbiome studies related to health outcomes. Diverse cohorts are needed to identify both population-specific responses to specific microbiome interventions and to achieve broader-reaching biological conclusions that generalize across populations.

The microbiome mediates the interaction between predation and heavy metals

Gut microbiota communities are fundamental ecological components in the aquatic food web. Their potential to mediate how organisms respond to multiple environmental stressors remains understudied. Here we explored how manipulations of the gut microbiome of Daphnia pulex, a keystone species in aquatic communities, influenced life history (size at maturity, age at maturity, somatic growth rate and clutch size), morphology (induced defence) and body condition (lipid status deposits) responses to combined anthropogenic (copper) and natural (predation risk) stress. Data from a factorial experiment revealed that the effect of predation risk on traits was often mediated by copper (predation risk and copper interact). These patterns align with theory linking predation risk and copper contamination via digestive physiology. We also found that each stressor, and their combination, was associated with the same community composition of the D. pulex microbiome. However, antibiotic manipulation of the microbiome reversed 7/12 the trait responses across life history, morphology and body condition. This was associated with dramatically different communities to control conditions, with clear and unique patterns of microbiome community composition for each stressor and their combination. Our study revealed that microbiome community composition is highly correlated with the response of organisms to multiple, simultaneous stressors.

Characterization and Selection of Lactobacillus plantarum and Lactobacillus paracasei for prevention of oral bacterial infections from Chinese pickle

The oral infections were mainly caused by Streptococci and Staphylococcus aureus. Antibiotic therapies can eliminate these harmful bacteria. However, it can break beneficial microbes and lead to the persistence of resistant strains. The objective of our study was to select potential probiotic strains for the prevention of oral bacterial infections and evaluate their potential probiotic properties in oral cavity. AR113 (Lactobacillus plantarum) and AR340 (Lactobacillus paracasei) with significantly antimicrobial β-hemolytic streptococci and Staphylococcus aureus activity were isolated from Chinese pickle through agar well diffusion assay. Through the analyses of probiotic properties in antibiofilm, lysozyme and hydrogen peroxide tolerance, bacterial surface properties, adherence ability, tooth degradation and anti-inflammatory activity, the AR113 and AR340 showed anti-adhesion activity of 45.2-71.1% and 20.3-56.8% against β-hemolytic streptococci and 15.4-52.6% and 30.7-65.9% against Staphylococcus aureus, respectively, at different concentration. The two strains with high hydrophobicity, autoaggregation and survival rate adhered strongly to FaDu cells. AR113 and AR340 exhibited low calcium released from teeth (0.04 μg/mL and 0.03 μg/mL, respectively). ELISA analysis showed that AR113 and AR340 significantly inhibited the LPS-induced increase of NO and TNF-α expression. Strains-fermented skim milk inhibited the growth of β-hemolytic streptococci or Staphylococcus aureus. AR113 and AR340 were considered as probiotic candidates because of their higher antibacterial activity against some oral pathogenic bacteria, no potential of primitive cariogenicity. These candidates were expected as new probiotics with potential oral health benefits and no harmful effects.

Bacterial Communities Associated With Four Blooming Scyphozoan Jellyfish: Potential Species-Specific Consequences for Marine Organisms and Humans Health

Cnidarians have large surface areas available for colonization by microbial organisms, which serve a multitude of functions in the environment. However, relatively few studies have been conducted on scyphozoan-associated microbial communities. Blooms of scyphozoan species are common worldwide and can have numerous deleterious consequences on the marine ecosystem. Four scyphozoan species, Aurelia coerulea, Cyanea nozakii, Nemopilema nomurai, and Rhopilema esculentum, form large blooms in Chinese seas. In this study, we analyzed the bacterial communities associated with these four jellyfish based on 16S rRNA gene sequencing. We found that the bacterial communities associated with each scyphozoan species were significantly different from each other and from those of the surrounding seawater. There were no significant differences between the bacterial communities associated with different body parts of the four scyphozoan jellyfish. Core bacteria in various compartments of the four scyphozoan taxa comprised 57 OTUs (Operational Taxonomic Units), dominated by genera Mycoplasma, Vibrio, Ralstonia, Tenacibaculum, Shingomonas and Phyllobacterium. FAPROTAX function prediction revealed that jellyfish could influence microbially mediated biogeochemical cycles, compound degradation and transmit pathogens in regions where they proliferate. Finally, Six genera of potentially pathogenic bacteria associated with the scyphozoans were detected: Vibrio, Mycoplasma, Ralstonia, Tenacibaculum, Nautella, and Acinetobacter. Our study suggests that blooms of these four common scyphozoans may cause jellyfish species-specific impacts on element cycling in marine ecosystems, and serve as vectors of pathogenic bacteria to threaten other marine organisms and human health.

Alterations of Gut Microbiota by Overnutrition Impact Gluconeogenic Gene Expression and Insulin Signaling

A high-fat, Western-style diet is an important predisposing factor for the onset of type 2 diabetes and obesity. It causes changes in gut microbial profile, reduction of microbial diversity, and the impairment of the intestinal barrier, leading to increased serum lipopolysaccharide (endotoxin) levels. Elevated lipopolysaccharide (LPS) induces acetyltransferase P300 both in the nucleus and cytoplasm of liver hepatocytes through the activation of the IRE1-XBP1 pathway in the endoplasmic reticulum stress. In the nucleus, induced P300 acetylates CRTC2 to increase CRTC2 abundance and drives Foxo1 gene expression, resulting in increased expression of the rate-limiting gluconeogenic gene G6pc and Pck1 and abnormal liver glucose production. Furthermore, abnormal cytoplasm-appearing P300 acetylates IRS1 and IRS2 to disrupt insulin signaling, leading to the prevention of nuclear exclusion and degradation of FOXO1 proteins to further exacerbate the expression of G6pc and Pck1 genes and liver glucose production. Inhibition of P300 acetyltransferase activity by chemical inhibitors improved insulin signaling and alleviated hyperglycemia in obese mice. Thus, P300 acetyltransferase activity appears to be a therapeutic target for the treatment of type 2 diabetes and obesity.

Interplay of Good Bacteria and Central Nervous System: Cognitive Aspects and Mechanistic Considerations

The human gastrointestinal tract hosts trillions of microorganisms that is called “gut microbiota.” The gut microbiota is involved in a wide variety of physiological features and functions of the body. Thus, it is not surprising that any damage to the gut microbiota is associated with disorders in different body systems. Probiotics, defined as living microorganisms with health benefits for the host, can support or restore the composition of the gut microbiota. Numerous investigations have proved a relationship between the gut microbiota with normal brain function as well as many brain diseases, in which cognitive dysfunction is a common clinical problem. On the other hand, increasing evidence suggests that the existence of a healthy gut microbiota is crucial for normal cognitive processing. In this regard, interplay of the gut microbiota and cognition has been under focus of recent researches. In the present paper, I review findings of the studies considering beneficial effects of either gut microbiota or probiotic bacteria on the brain cognitive function in the healthy and disease statuses.

Impact of dietary components on enteric infectious disease

Diets impact host health in multiple ways and an unbalanced diet could contribute to the initiation or progression of a variety of diseases. Although a wealth of information exists on the connections between diet and chronic metabolic diseases such as cardiovascular disease, diabetes mellitus, etc., how diet influences enteric infectious disease still remain underexplored. The review summarizes the current findings on the link between various dietary components and diverse enteric infectious diseases. Dietary ingredients discussed include macronutrients (carbohydrates, lipids, proteins), micronutrients (vitamins, minerals), and other dietary ingredients (phytonutrients and probiotic supplements). We first describe the importance of enteric infectious diseases and the direct and indirect relationship between diet and enteric infectious diseases. Then we discuss the effects of different dietary components on the susceptibility to or progression of enteric infectious disease. Finally, we delineate current knowledge gap and highlighted future research directions. The literature review revealed that different dietary components affect host resistance to enteric infections through a variety of mechanisms. Dietary components may directly inhibit or bind to enteric pathogens, or indirectly influence enteric infections through modulating immune function and gut microbiota. Elucidating the unique repercussions of different diets on enteric infections in this review may help provide dietary guidelines or design dietary interventions to prevent or alleviate enteric infectious diseases.

Gut Microbiota and Diarrhea: An Updated Review

Diarrhea is a common problem to the whole world and the occurrence of diarrhea is highly associated with gut microbiota, such as bacteria, fungi, and viruses. Generally, diarrheal patients or animals are characterized by gut microbiota dysbiosis and pathogen infections may lead to diarrheal phenotypes. Of relevance, reprograming gut microbiota communities by dietary probiotics or fecal bacteria transplantation are widely introduced to treat or prevent diarrhea. In this review, we discussed the influence of the gut microbiota in the infection of diarrhea pathogens, and updated the research of reshaping the gut microbiota to prevent or treat diarrhea for the past few years. Together, gut microbiota manipulation is of great significance to the prevention and treatment of diarrhea, and further insight into the function of the gut microbiota will help to discover more anti-diarrhea probiotics.

High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs

High fat diets have been reported to negatively affect the microbiota in both mice and humans. However, there is a lack of studies in canine models. The variation among the gastrointestinal (GI) tract anatomy/physiology and typical diet compositions of these animal species may lead to vastly different results. Due to the large inclusion rate of dietary fat in pet food, it is critical to understand its effects in a canine model. Therefore, the study objective was to report the effects of high fat, low carbohydrate diets on the fecal microbiota in healthy adult dogs. Eight adult beagles were randomly assigned to one of four dietary treatments within each 15-day period of a replicated 4x4 Latin Square design. Diets contained 32% (T1), 37% (T2), 42% (T3), and 47% (T4) fat. T2, T3, and T4 were created by adding increasing levels of canola oil to T1, a commercially manufactured canned canine diet, which served as the control diet. Fresh fecal samples were collected during the last 5 days of each period for microbial analysis. DNA was extracted from fecal samples and paired-end 16S rRNA gene amplicon sequencing was performed using the Illumina MiSeq platform. When comparing whole microbial communities using PERMANOVA, no significant differences were observed among treatments (P = 0.735). Individual OTUs were analyzed using the GLIMMIX procedure of SAS with fixed effects of diet and room, and the random effects of period and animal. Out of the 100 most abundant individual OTUs, 36 showed significant differences in abundance based on treatment (q < 0.05). Overall, OTUs assigned to genera related to fat digestion increased while OTUs assigned to genera involved in carbohydrate digestion decreased. In conclusion, the microbial community adapted to dietary intervention without jeopardizing the health of the animals, evaluated by body condition score, fecal characteristics, and blood parameters.

Microbial diversity and structure in the gastrointestinal tracts of two stranded short-finned pilot whales (Globicephala macrorhynchus) and a pygmy sperm whale (Kogia breviceps)

Information on the gut microbiome composition of different mammals could provide novel insights into the evolution of mammals and succession of microbial communities in different hosts. However, there is limited information on the gut microbiome composition of marine mammals, especially cetaceans because of sampling constraints. In this study, we investigated the diversity and composition of microbial communities in the stomach, midgut, and hindgut of 2 stranded short‐finned pilot whales (Globicephala macrorhynchus) and hindgut of a stranded pygmy sperm whale (Kogia breviceps) by using 16S rRNA gene amplicon sequencing technology. On the basis of the 50 most abundant operational taxonomic units, principal coordinate analysis, and non‐metric multidimensional scaling analysis, we confirmed that the gut microbial communities of the 3 whales were different. Our results revealed that the gut microbiome of 1 stranded short‐finned pilot whale GM16 was dominated by Firmicutes (mainly Clostridium) and Fusobacteria; whereas that of the other pilot whale GM19 was composed of Gammaproteobacteria and Bacteroidetes (mainly Vibrio and Bacteroides, respectively), probably caused by intestinal disease and antibiotic treatment. The gut microbiome of the pygmy sperm whale was dominated by Firmicutes and Bacteroidetes. Moreover, different gastrointestinal tract regions harbored different microbial community structures. To our knowledge, this is the first report of the gut microbiome of short‐finned pilot whales, and our findings will expand our current knowledge on microbial diversity and composition in the gastrointestinal tract of cetaceans.

Alternatives to antibiotics in a One Health context and the role genomics can play in reducing antimicrobial use

BACKGROUND

This review follows on from the International Conference on One Health Antimicrobial Resistance (ICOHAR 2019), where strategies to improve the fundamental understanding and management of antimicrobial resistance at the interface between humans, animals and the environment were discussed.

OBJECTIVE

This review identifies alternatives to antimicrobials in a One Health context, noting how advances in genomic technologies are assisting their development and enabling more targeted use of antimicrobials.

SOURCES

Key articles on the use of microbiota modulation, livestock breeding and gene editing, vaccination, antivirulence strategies and bacteriophage therapy are discussed.

CONTENT

Antimicrobials are central for disease control, but reducing their use is paramount as a result of the rise of transmissible antimicrobial resistance. This review discusses antimicrobial alternatives in the context of improved understanding of fundamental host-pathogen and microbiota interactions using genomic tools.

IMPLICATIONS

Host and microbial genomics and other novel technologies play an important role in devising disease control strategies for healthier animals and humans that in turn reduce our reliance on antimicrobials.

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study

Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.

A polysaccharide from Fagopyrum esculentum Moench bee pollen alleviates microbiota dysbiosis to improve intestinal barrier function in antibiotic-treated mice

Antibiotics are the most commonly used clinical drugs for anti-infection, but they can also destroy normal microorganisms and cause intestinal barrier dysfunction. To elucidate the effects and mechanism of a water-soluble polysaccharide from Fagopyrum esculentum Moench bee pollen (WFPP) on intestinal barrier integrity in antibiotic-treated mice, BALB/c mice were exposed to a broad-spectrum antibiotic (ceftriaxone) or not (control), and were administered low-, medium- and high-dose WFFP (100 mg kg^-1, 200 mg kg^-1 and 400 mg kg^-1, respectively) daily by oral gavage for 3 weeks. Mice treated with ceftriaxone displayed symptoms of growth retardation, atrophy of immune organs including thymus and spleen, increased gut permeability, and intestinal barrier damage, which were restored after intervention with WFFP at different doses. Moreover, the beneficial effects of WFFP were closely associated with enhanced intestinal sIgA secretion and reduced inflammatory response. Furthermore 16S rDNA gene sequencing revealed that WFPP elevated microbial diversity and richness and changed the community structure, therefore, alleviating microbiota dysbiosis caused by ceftriaxone. Interestingly, WFPP could modulate the abundance of sIgA secretion-related bacteria (e.g. Proteobacteria) and inflammation-related bacteria (e.g. Enterococcus). Therefore, WFPP can relieve antibiotic-induced microbiota dysbiosis to improve intestinal barrier integrity by increasing intestinal sIgA secretion and inhibiting inflammation.

Gut Microbiota and Epilepsy: A Systematic Review on Their Relationship and Possible Therapeutics

Dysbiosis of gut microbiota may lead to a range of diseases including neurological disorders. Thus, it is hypothesized that regulation of the intestinal microbiota may prevent or treat epilepsy. The purpose of this systematic review is to evaluate the evidence investigating the relationship between gut microbiota and epilepsy and possible interventions. A systematic review of the literature was done on four databases (PubMed, Scopus, EMBASE, and Web of Science). Study selection was restricted to original research articles while following the PRISMA guidelines. Six studies were selected. These studies cohesively support the interaction between gut microbiota and epileptic seizures. Gut microbiota analysis identified increases in Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria with decreases in Bacteroidetes and Actinobacteria in epileptic patients. Ketogenic diet, probiotics, and fecal microbiota transplantation (FMT) improved the dysbiosis of the gut microbiota and seizure activity. However, the studies either had a small sample size, lack of subject variability, or short study or follow-up period, which may question their reliability. Nevertheless, these limited studies conclusively suggest that gut microbiota diversity and dysbiosis may be involved in the pathology of epilepsy. Future studies providing more reliable and in depth insight into the gut microbial community will spark promising alternative therapies to current epilepsy treatment.

Competitive reduction of poultry-borne enteric bacterial pathogens in chicken gut with bioactive Lactobacillus casei

In this study, the effect of sustainable probiotics on Campylobacter jejuni colonization and gut microbiome composition was evaluated using chicken as a model organism. Chickens were given Lactobacillus casei over-expressing myosin-cross-reactive antigen (LC+mcra). LC+mcra can generate bioactive compounds in larger quantity including conjugated linoleic acid. A total of 120 chickens were used in duplicate trials to investigate the effectiveness of LC+mcra in decreasing C. jejuni colonization by means of kanamycin resistant strain compared to the control group. We observed that LC+mcra can efficiently colonize various parts of the chicken gut and competitively reduce colonization of natural and challenged C. jejuni and natural Salmonella enterica. LC+mcra was found to reduce C. jejuni colonization in cecum, ileum and jejunum, by more than one log CFU/g when compared to the no-probiotic control group. Furthermore, 16S rRNA compositional analysis revealed lower abundance of Proteobacteria, higher abundance of Firmicutes, along with enriched bacterial genus diversity in gut of LC+mcra fed chicken. Decreased contamination of drinking water by C. jejuni and S. enterica was also observed, suggesting a potential function of reducing horizontal transfer of enteric bacteria in poultry. Outcomes of this study reveal high potential of LC+mcra as sustainable approach to decrease colonization of C. jejuni and S. enterica in poultry gut along with other beneficial attributes.