Protective role of gut commensal microbes against intestinal infections

Probiotics for inflammatory bowel disease: Is there sufficient evidence?

Inflammatory bowel disease (IBD) refers to chronic inflammatory disorders of the gut. Ulcerative colitis (UC) and Crohn's disease (CD) are two subtypes of IBD. Evidence suggests that the intestinal microbiota plays a role in the pathogenesis of IBD, so probiotics have garnered a lot of interest as a potential treatment or prevention for IBD. However, clinical evidence of the efficacy of probiotics is still debatable. We performed a literature review. An advanced search considered clinical studies on probiotic for IBD from inception to 2023 in PubMed, Embase, Cochrane Library, and Web of Science. In the treatment of UC with probiotics, only Escherichia coli Nissle 1917 for maintenance treatment of UC in remission, and Bifidobacterium and VSL#3 for induction of remission in patients with mild to moderately active UC have shown strong evidence. Currently, there are no definitive conclusions regarding the effectiveness of probiotics in CD. The mechanism of probiotic treatment for IBD may be related to reducing oxidative stress, repairing the intestinal barrier, regulating intestinal flora balance, and modulating intestinal immune response. Differences in the benefits of probiotics between CD and UC may be attributable to the different lesion extent and immune-mediated pathophysiology. More robust randomized clinical trials are required to validate the efficacy and safety of diverse probiotic strains in IBD.

Glycolysis characteristics of intracellular polysaccharides from Agaricus bitorquis (Quél.) sacc. Chaidam and its effects on intestinal flora from different altitudes of mice in vitro fermentation

The glycolysis characteristics and effects on intestinal flora of polysaccharides from Agaricus bitorquis (Quél.) Sacc. Chaidam (ABIPs) in vitro fermentation by different altitudes of mice feces was examined, including low, medium, and high altitudes groups (LG, MG, and HG). In vitro, fermentation of ABIPs forty-eight hours resulted in a remarkable decrease in total sugar content and improvement of short-chain fatty acids (SCFAs) (mainly acetate, propionate, and butyrate), which simultaneously induced the composition of monose and uronic acids and SCFAs continuously change. Besides, ABIPs influenced the abundance and composition of the intestinal flora, generally increasing the abundance of probiotic bacteria (such as Bifidobacterium and Faecalibacterium) and decreasing the abundance of harmful bacteria (such as Phenylobacterium and Streptococcus) in all groups, with the highland biology core genus Blautia significantly enriched in LG and MG groups. It was also found that ABIPs enhanced pathways associated with biosynthesis and metabolism. In addition, correlation analysis speculated that the metabolism of SCFAs by ABIPs may be associated with genera such as Anaerostipes, Roseburia, and Weissella. ABIPs may protect organismal health by regulating hypoxic intestinal flora composition and metabolic function, and more superior fermentation performance was observed in MG compared to other groups.

The resistome and microbiome of wastewater treatment plant workers - The AWARE study

Urban wastewater treatment plants harbor a large collection of antibiotic resistant enteric bacteria. It is therefore reasonable to hypothesize that workers at such plants would possess a more diverse set of resistant enteric bacteria, compared to the general population. To address this hypothesis, we have compared the fecal microbiome and resistome of 87 workers at wastewater treatment plants (WWTPs) from Romania and the Netherlands to those of 87 control individuals, using shotgun metagenomics. Controlling for potential confounders, neither the total antibiotic resistance gene (ARG) abundance, nor the overall bacterial composition were significantly different between the two groups. If anything, the ARG richness was slightly lower in WWTP workers, and in a stratified analysis the total ARG abundance was significantly lower in Dutch workers compared to Dutch control participants. We identified country of residence, together with recent antibiotic intake in the Dutch population, as the largest contributing factors to the total abundance of ARGs. A striking side-finding was that sex was associated with carriage of disinfectant resistance genes, with women in both Romania and the Netherlands having significantly higher abundance compared to men. A follow up investigation including an additional 313 publicly available samples from healthy individuals from three additional countries showed that the difference was significant for three genes conferring resistance to chemicals commonly used in cosmetics and cleaning products. We therefore hypothesize that the use of cosmetics and, possibly, cleaning products leads to higher abundance of disinfectant resistance genes in the microbiome of the users. Altogether, this study shows that working at a WWTP does not lead to a higher abundance or diversity of ARGs and no large shifts in the overall gut microbial composition in comparison to participants not working at a WWTP. Instead, other factors such as country of residence, recent antibiotic intake and sex seem to play a larger role.

Effects of Clostridium butyricum on Growth Performance, Intestinal Health, and Disease Resistance of Hybrid Grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) Fed with Cottonseed Protein Concentrate (CPC) Replacement of Fishmeal

An 8-week feeding trial was conducted to investigate the effects of C. butyricum on the growth performance, microbiota, immunity response, and disease resistance in hybrid grouper fed with cottonseed protein concentrate (CPC) replacement of fishmeal. Six groups of isonitrogenous and isolipid diets were formulated including a positive control group (50% fishmeal, PC), a negative control group (CPC replaced 50% of fishmeal protein, NC), and Clostridium butyricum supplemented with 0.05% (C1, 5 × 10⁸ CFU/kg), 0.2% (C2, 2 × 10⁹ CFU/kg), 0.8% (C3, 8 × 10⁹ CFU/kg), and 3.2% (C4, 3.2 × 10¹⁰ CFU/kg), respectively, to the NC group. The results showed that weight gain rate and specific growth rate were significantly higher in the C4 group than that in the NC group (P < 0.05). After supplementation with C. butyricum, the amylase, lipase, and trypsin activities were significantly higher than the NC group (P < 0.05; except group C1), and the same results were obtained for intestinal morphometry. The intestinal proinflammatory factors were significantly downregulated, and the anti-inflammatory factors were significantly upregulated in the C3 and C4 groups compared with the NC group after supplementation with 0.8%-3.2% C. butyricum (P < 0.05). At the phylum level, the PC, NC, and C4 groups were dominated by the Firmicutes and the Proteobacteria. At the genus level, the relative abundance of Bacillus in the NC group was lower than that in the PC and C4 groups. After supplementation with C. butyricum, grouper in the C4 group showed significantly higher resistance to V. harveyi than the NC group (P < 0.05). Above all, taking into account the effects of immunity and disease resistance, it was recommended to supplement 3.2% C. butyricum in the diet of grouper fed the replacement of 50% fishmeal protein by CPC.

Mass spectrometric analysis of bioactive conditioned media of bacteria isolated from reptilian gut

Aim

To determine whether selected gut bacteria of crocodile exhibit antibacterial properties.

Materials & methods

Two bacteria isolated from Crocodylus porosus gut were used, namely: Pseudomonas aeruginosa and Aeromonas dhakensis. Conditioned media were tested against pathogenic bacteria and metabolites were analyzed using liquid chromatography-mass spectrometry.

Results & conclusion

Antibacterial assays revealed that conditioned media showed potent effects against pathogenic Gram-positive and Gram-negative bacteria. LC-MS revealed identity of 210 metabolites. The abundant metabolites were, N-Acetyl-L-tyrosine, Acetaminophen, Trans-Ferulic acid, N, N-Dimethylformamide, Pyrocatechol, Cyclohexanone, Diphenhydramine, Melatonin, Gamma-terpinene, Cysteamine, 3-phenoxypropionic acid, Indole-3-carbinol, Benzaldehyde, Benzocaine, 2-Aminobenzoic acid, 3-Methylindole. These findings suggest that crocodile gut bacteria are potential source of novel bioactive molecules that can be utilized as pre/post/antibiotics for the benefit of human health.

Alteration of the Gut Microbiota in Missed Abortion

There is a symbiotic relationship between gut microbiota and human beings. Imbalance of the gut microbiota will cause pathological damages to humans. Although many risk factors are associated with missed abortion (MA), the pathological mechanism of it is still unclear. Here, we analyzed gut flora of the patients with MA by S16 high-throughput sequencing. The possible pathogenic mechanisms of the MA were explored. Fecal samples from 14 healthy controls and 16 MA patients were collected to do 16S rRNA gene high-throughput sequencing analysis. The abundance of the Bacteroidetes, Proteobacteria, Actinobacteria, Escherichia, Streptococcus_ Salivarius, and Lactobacillus was significantly reduced in the MA group, while, the abundance of the Klebsiella was significantly increased in the MA patients. The Ruminococcaceae and [Eubacterium]_coprostanoligenes_group were found only in the specimens of the MA patients. The Fabrotax function prediction analysis showed that four photosynthesis function bacteria (cyanobateria, oxygenic_photoautotrophy, photoautotrophy, and phototrophy) only existed in the MA group. In the analysis of the BugBase microbiome function prediction, the Escherichia of the MA group is significantly reduced compared to that of the healthy controls in the items of that Contains_Mobile_Elements, Facultatively_Anaerobic, Forms_Biofilms, Potentially_Pathogenic.png, Gram_Nagative, and Stress_Tolerant_relabundance. These alterations may affect the stability of the host's immune, neural, metabolic and other systems by interfering with the balance of the gut microbiota or by the metabolites of those bacteria, causing the MA. This study explored the possible pathogenic factors of the gut microbiota of the MA. The results provide evidence to figure out the pathogenesis of the MA.

Early Weaning Stress Induces Intestinal Microbiota Disturbance, Mucosal Barrier Dysfunction and Inflammation Response Activation in Pigeon Squabs

Early weaning stress has been reported to impair intestinal health in mammals. Like mammals, weaning of the pigeon squab, an altricial bird, is associated with social, environmental and dietary stress. However, understanding of weaning stress on intestinal functions is very limited in altricial birds, especially in squabs. This study was aimed to evaluate the effects of early weaning stress on intestinal microbiota diversity, architecture, permeability, the first line defense mechanisms, mucosal barrier functions, and immune cell responses. A total of 192 newly hatched squabs were randomly allocated into two groups, one weaned on day 7 and the other remained with the parent pigeons. Mucosal tissue and digesta in ileum, as well as blood samples, were collected from squabs (n = 8) on days 1, 4, 7, 10, and 14 postweaning. Our results showed that weaning stress induced immediate and long-term deleterious effects on both growth performance and intestinal barrier functions of squabs. Early weaning significantly increased ileal bacterial diversity and alters the relative abundance of several bacteria taxa. Weaning stress can also cause morphological and functional changes in ileum, including an atrophy in villi, an increase in permeability, and a variation in the mRNA expression of genes encoding mucins, immunoglobulins, tight junction proteins, toll-like receptors, and cytokines, as well as the concentration of secretory IgA. We concluded that the impaired intestinal barrier functions accompanied with early weaning stress seems to be the main reason for the poor growth rate after weaning in squabs. In addition, the disturbance of intestinal microbiota of early weaning stress in squabs coincided with dysfunction of intestinal mucosal barrier and activation of inflammation cell responses that were possibly mediated via the activation of toll-like receptors.

The role of γδ T cells in the interaction between commensal and pathogenic bacteria in the intestinal mucosa

The intestinal mucosa is an important structure involved in resistance to pathogen infection. It is mainly composed of four barriers, which have different but interrelated functions. Pathogenic bacteria can damage these intestinal mucosal barriers. Here, we mainly review the mechanisms of pathogen damage to biological barriers. Most γδ T cells are located on the surface of the intestinal mucosa, with the ability to migrate and engage in crosstalk with microorganisms. Commensal bacteria are involved in the activation and migration of γδ T cells to monitor the invasion of pathogens. Pathogen invasion alters the migration pattern of γδ T cells. γδ T cells accelerate pathogen clearance and limit opportunistic invasion of commensal bacteria. By discussing these interactions among γδ T cells, commensal bacteria and pathogenic bacteria, we suggest that γδ T cells may link the interactions between commensal bacteria and pathogenic bacteria.

Gut barrier disruption and chronic disease

The intestinal barrier protects the host against gut microbes, food antigens, and toxins present in the gastrointestinal tract. However, gut barrier integrity can be affected by intrinsic and extrinsic factors, including genetic predisposition, the Western diet, antibiotics, alcohol, circadian rhythm disruption, psychological stress, and aging. Chronic disruption of the gut barrier can lead to translocation of microbial components into the body, producing systemic, low-grade inflammation. While the association between gut barrier integrity and inflammation in intestinal diseases is well established, we review here recent studies indicating that the gut barrier and microbiota dysbiosis may contribute to the development of metabolic, autoimmune, and aging-related disorders. Emerging interventions to improve gut barrier integrity and microbiota composition are also described.

Modulation of Intestinal Barrier, Inflammatory Response, and Gut Microbiota by Pediococcus pentosaceus zy-B Alleviates Vibrio parahaemolyticus Infection in C57BL/6J Mice

Modulation of the intestinal barrier, inflammation, and gut microbiota by Pediococcus pentosaceus zy-B (zy-B) in Vibrio parahaemolyticus (Vp)-infected C57BL/6J mice was studied. Mice intragastrically pretreated with 10⁸ colony-forming units (CFU) zy-B significantly alleviated Vp infection as evidenced by maintaining body weight and reduced disease activity index score and intestine ratio. In addition, zy-B reduced the Vp load in the ileum and cecum, significantly reduced the load in the colon, prevented colonic atrophy, and strengthened mucosal integrity. Mechanistically, zy-B ameliorated intestinal barrier dysfunction by upregulating tight junction protein expression, which in turn reduced the lipopolysaccharide, d-lactic acid (d-LA), and diamine oxidase concentrations and downregulated the cannabinoid receptor 1 (CB1) and CB2 mRNA expressions. Moreover, zy-B systemically reduced inflammation by decreasing interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α levels, and increased interleukin-10 (IL-10), immunoglobulin M (IgM), and immunoglobulin G (IgG) levels in the colon and serum. Furthermore, zy-B markedly altered the gut microbiota composition by enriching Bifidobacterium, Akkermansia, and Lactobacillus in the colon. Overall, zy-B appears to act as a probiotic to alleviate Vp infection by protecting the intestinal barrier, reducing inflammation, and promoting the growth of "beneficial" gut microbiota.

Developmental changes of nutrient digestion in young lambs are influenced by weaning and associated with intestinal microbiota

Understanding the effects of weaning on the changes of digestive function could help to design efficient intervention strategies for promoting the development of the lamb during the early stages of life. In this study, 24 lambs were divided into two groups (control group, lambs were not weaned; and weaning group, lambs were weaned at 21 days of age). The growth, nutrient digestion, gastrointestinal enzyme activity, plasma biochemical indicators, and intestinal microbiota at 7-49 days were determined, as well as the impact of early weaning. The nutrient digestion changed rapidly with age, especially at 14-28 days (p < 0.05). Weaning reduced the dry matter (DM), crude protein (CP), and ether extract (EE) intake and digestion, but increased the starch, neutral detergent fiber (NDF), and acid detergent fiber (ADF) intake and digestion (p < 0.05). Weaning did not affect the overall jejunal microbiota (p > 0.05), but affected the relative abundance of certain bacteria taxa (p < 0.05). Lactic acid-producing bacteria, such as Olsenella, Bacillus, Sharpea, and Bifidobacterium are closely related to CP or EE digestion and growth performance (p < 0.05). In summary, we delineated the pattern of nutrient digestion and intestinal microbiota development in young lambs, and the impact of early weaning.

Effects of red ginseng extract on gut microbial distribution

Background

Red ginseng extract boosts immunity against inflammation and cancer in the human body. However, studies on the effects of red ginseng extract on the gut microbiome remain unexplored.

Methods

In 2019, the positive effects and changes in the gut microbiome after administering 1 pack (3 g) of red ginseng extract per day to 53 adults aged 40 to 75 for 24 weeks were investigated. The gut microbial environment changes were qualitatively and quantitatively analyzed using next-generation sequencing and real-time polymerase chain reaction technology.

Results

On comparing and analyzing alpha diversity and beta diversity, the microbial pattern showed significant differences (OTUs p = 0.003, chao1 p < 0.001, Bray-Curtis p = 0.001) before and after ingestion of red ginseng extract, indicating that gut microbial richness increased after ingestion. Moreover, after comparing and analyzing the gut microbiome's differences after red ginseng extract intake, significant differences were noted between three strains at the phylum level and among 57 strains at the genus level.

Conclusion

This study proposes the potential use of red ginseng extract as a prebiotic after confirming its positive effects, including increasing gut microbiome richness, reducing harm to the gut microbiome, and increasing the number of some strains in the gut microbiome.

Progress and prospects of the healthy human gut virome

Not all viruses associated with humans cause disease. Non-pathogenic human-infecting viruses are predicted as important for immune system induction and preparation. Phages that infect bacteria are the most abundant predators of the human microbial ecosystem, promoting and maintaining bacterial diversity. Metagenomic analyses of the human gut virome and microbiome are unravelling the intricate predator-prey dynamics of phage-bacteria co-existence, co-evolution, and their interplay with the human host. While most adults harbour a distinctly individualistic and persistent community of virulent phages, new-borns are dominated by temperate phages heavily influenced by environmental exposures. The future development of microbiome-based interventions, therapeutics, and manipulation, will require a greater understanding of the human microbiome and the virome.

An Escherichia coli strain with extra catalase activity protects against murine colitis by scavenging hydrogen peroxide and regulating regulatory t cell/interleukin-17 pathways

BACKGROUND

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract whose occurrence is attributed to various factors, including genetic factors, immune response, microbial changes, and oxidative stress. Microbial-targeted therapy has emerged as an alternative to immunosuppressive therapy for IBD.

METHODS

The effects of an atypical commensal Escherichia coli strain harboring an additional catalase gene (compared to typical E. coli strain) on dextran sulfate sodium (DSS)-induced colitis were explored in mice.

RESULTS

The atypical E. coli (atEc) significantly restored body weight, reduced disease activity score, and improved histological scores in mice with colitis. Hydrogen peroxide levels in colitis mice were noticeably decreased when the mice were administered atEc. The proinflammatory cytokine levels were decreased and regulatory T cell numbers were increased after the administration of atEc. The abundance of Firmicutes was significantly recovered, while that of Proteobacteria decreased in atEc -treated mice compared with that in vehicle-treated wild-type mice. To investigate the role of interleukin (IL)-17A in mediating the anti-inflammatory effects of the atEc, IL-17A‒knockout mice were orally administered atEc. Clinical and immune responses and microbial composition were significantly reduced in IL-17A‒knockout mice compared with those in wild-type mice.

CONCLUSIONS

atEc ameliorates colonic inflammation by controlling hydrogen peroxide levels, immune responses (including regulatory T cells and IL-17A), and microbial composition. atEc could be a novel candidate of probiotic for IBD treatment.

Description of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birds

Phenotypic and genomic analyses were performed to characterize two novel species, H23M54^T and AMA3305^T, isolated from the faeces of the Oriental stork (Ciconia boyciana) and the cinereous vulture (Aegypius monachus), respectively. Strains H23M54^T and AMA3305^T showed the highest similarities of 16S rRNA gene sequences and complete genome sequences with Ornithinimicrobium cavernae CFH 30183^T (98.5% of 16S rRNA gene sequence similarity and 82.1% of average nucleotide identity, ANI) and O. pekingense DSM 21552^T (98.5% of 16S rRNA gene sequence similarity and 82.3% of ANI), respectively. Both strains were Gram-stain-positive, obligate aerobes, non-motile, non-spore-forming, and coccoid- and rodshaped. Strain H23M54^T grew optimally at 25-30°C and pH 8.0 and in the presence of 1.5-2% (wt/vol) NaCl, while strain AMA3305^T grew optimally at 30°C and pH 7.0 and in the presence of 1-3% (wt/vol) NaCl. Both strains had iso-C_15:0, iso-C_16:0, and summed feature 9 (iso-C_17:1ω9c and/or C_16:0 10-methyl) as major cellular fatty acids. MK-8 (H₄) was identified as the primary respiratory quinone in both strains. Strains H23M54^T and AMA3305^T possessed diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. Moreover, strains H23M54^T and AMA3305^T commonly contained ribose and glucose as major sugars and L-ornithine, L-alanine, glycine, and aspartic acid as major amino acids. The polyphasic taxonomic data indicate that strains H23M54^T and AMA3305^T represent novel species of the genus Ornithinimicrobium. We propose the names Ornithinimicrobium ciconiae sp. nov. and Ornithinimicrobium avium sp. nov. for strains H23M54^T (= KCTC 49151^T = JCM 33221^T) and AMA3305^T (= KCTC 49180^T = JCM 32873^T), respectively.

Stimulation of Toll-Like Receptor 3 Diminishes Intracellular Growth of Salmonella Typhimurium by Enhancing Autophagy in Murine Macrophages

The Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative Gram-negative bacterium that causes acute gastroenteritis and food poisoning. S. Typhimurium can survive within macrophages that are able to initiate the innate immune response after recognizing bacteria via various pattern-recognition receptors (PRRs), such as Toll-like receptors (TLRs). In this study, we investigated the effects and molecular mechanisms by which agonists of endosomal TLRs—especially TLR3—contribute to controlling S. Typhimurium infection in murine macrophages. Treatment with polyinosinic:polycytidylic acid (poly(I:C))—an agonist of TLR3—significantly suppressed intracellular bacterial growth by promoting intracellular ROS production in S. Typhimurium-infected cells. Pretreatment with diphenyleneiodonium (DPI)—an NADPH oxidase inhibitor—reduced phosphorylated MEK1/2 levels and restored intracellular bacterial growth in poly(I:C)-treated cells during S. Typhimurium infection. Nitric oxide (NO) production increased through the NF-κB-mediated signaling pathway in poly(I:C)-treated cells during S. Typhimurium infection. Intracellular microtubule-associated protein 1A/1B-light chain 3 (LC3) levels were increased in poly(I:C)-treated cells; however, they were decreased in cells pretreated with 3-methyladenine (3-MA)—a commonly used inhibitor of autophagy. These results suggest that poly(I:C) induces autophagy and enhances ROS production via MEK1/2-mediated signaling to suppress intracellular bacterial growth in S. Typhimurium-infected murine macrophages, and that a TLR3 agonist could be developed as an immune enhancer to protect against S. Typhimurium infection.

The Role of Gut Barrier Dysfunction and Microbiome Dysbiosis in Colorectal Cancer Development

Accumulating evidence indicates that breakdown of the+ protective mucosal barrier of the gut plays a role in colorectal cancer (CRC) development. Inflammation and oxidative stress in the colonic epithelium are thought to be involved in colorectal carcinogenesis and the breakdown of the integrity of the colonic barrier may increase the exposure of colonocytes to toxins from the colonic milieu, enhancing inflammatory processes and release of Reactive Oxygen Species (ROS). The aetiological importance of the gut microbiome and its composition - influenced by consumption of processed meats, red meats and alcoholic drinks, smoking, physical inactivity, obesity - in CRC development is also increasingly being recognized. The gut microbiome has diverse roles, such as in nutrient metabolism and immune modulation. However, microbial encroachment towards the colonic epithelium may promote inflammation and oxidative stress and even translocation of species across the colonic lumen. Recent research suggests that factors that modify the above mechanisms, e.g., obesity and Western diet, also alter gut microbiota, degrade the integrity of the gut protective barrier, and expose colonocytes to toxins. However, it remains unclear how obesity, lifestyle and metabolic factors contribute to gut-barrier integrity, leading to metabolic disturbance, colonocyte damage, and potentially to CRC development. This review will discuss the interactive roles of gut-barrier dysfunction, microbiome dysbiosis, and exposure to endogenous toxins as another mechanism in CRC development, and how biomarkers of colonic mucosal barrier function may provide avenues for disease, prevention and detection.

Gut Microbiota: From the Forgotten Organ to a Potential Key Player in the Pathology of Alzheimer's Disease

More than 300 years ago, Antony van Leewenhoeck first described observing single-celled microorganisms, which he termed “animalcules,” examining his saliva under a microscope. Although the idea of the coexistence of microorganisms in our body is not new, we have only recently been able to investigate their ecological relationship to our body, with the development of high-throughput molecular techniques. The diverse microorganism communities residing in our guts are established and maintained by complex interactions among microorganisms and their host. Notably, their alteration has been implicated in influencing various diseases including neurological diseases. Alzheimer’s disease (AD) is the most common cause of dementia characterized by a progressive decline in memory and thinking severe enough to interfere with daily life. Despite the great progress in linking genetic risk factors with AD pathogenesis, treatments targeted at AD pathology and its modifiers have not yet resulted in a disease-modifying therapy. There is mounting evidence that the gut microbiota interacts with AD pathogenesis by disrupting neuroinflammation and metabolic homeostasis—the gut microbiota has gone from being the forgotten organ to a potential key player in the AD pathology.

Interactions Between Rumen Microbes, VFAs, and Host Genes Regulate Nutrient Absorption and Epithelial Barrier Function During Cold Season Nutritional Stress in Tibetan Sheep

As one of the important ruminants of the Qinghai-Tibet Plateau, Tibetan sheep are able to reproduce and maintain their population in this harsh environment of extreme cold and low oxygen. However, the adaptive mechanism of Tibetan sheep when nutrients are scarce in the cold season of the Plateau environment is unclear. We conducted comparative analysis rumen fermentation parameters, rumen microbes, and expression of host genes related to nutrient absorption and rumen epithelial barrier function in cold and warm season Tibetan sheep. We found that concentrations of the volatile fatty acids (VFAs) acetate, propionate and butyrate of Tibetan sheep in the cold season were significantly higher than in the warm season (P < 0.05). Microbial 16S rRNA gene analysis revealed significant differences in rumen microbiota between the cold and warm seasons, and the abundance of microbial in the cold season was significantly higher than that in the warm season (P < 0.05), and the lack of nutrients in the cold season led to a significant reduction in the expression of SGLT1, Claudin-4, and ZO-1 genes in the rumen epithelium. Correlation analysis revealed significant associations of some rumen microorganisms with the fermentation product acetate and the rumen epithelial genes SGLT1, Claudin-4, and ZO-1.

Microbiota-host interactions shape ageing dynamics

Occupying the interface between host and environment, host-associated microbes play fundamental roles in nutrient absorption, essential metabolite synthesis, development of the immune system, defence against pathogens and pathogenesis. Microbiota composition and function is rather stable during adulthood, while it dramatically changes during early development, frailty and disease. Ageing is associated with progressive decrease of homeostasis, often resulting in disruption of the physiological balance between host and commensal microbes, ultimately leading to dysbiosis and host demise. Generally, high microbial diversity is associated with health and a youthful state, while low individual microbial diversity and larger inter-individual microbial diversity is associated with ageing and disease states. Different species are equipped with species-specific commensal, symbiotic and pathogenic microbial communities. How and whether the specific host-microbiota consortia co-evolved with host physiology to ensure homeostasis and promote individual fitness remains an open question. In this essay, we propose that the evolution of vertebrate-specific immune adaptations may have enabled the establishment of highly diverse, species-specific commensal microbial communities. We discuss how the maintenance of intact immune surveillance mechanisms, which allow discrimination between commensal and pathogenic bacteria, fail during ageing and lead to the onset of known ageing-related diseases. We discuss how host-microbiota interactions are key to maintaining homeostasis despite external perturbations, but also how they affect a range of host-specific ageing-related phenotypes. This article is part of the theme issue 'The role of the microbiome in host evolution'.

Cholangiocyte derived carcinomas and local microbiota

Trillions of bacteria are present in the gastrointestinal tract as part of the local microbiota. Bacteria have been associated with a wide range of gastrointestinal diseases including malignant neoplasms. The association of bacteria in gastrointestinal and biliary tract carcinogenesis is supported in the paradigm of Helicobacter pylori and intestinal-type gastric cancer. However, the association of bacterial species to a specific carcinoma, different from intestinal-type gastric cancer is unresolved. The relationship of bacteria to a specific malignant neoplasm can drive clinical interventions. We review the classic bacteria risk factors identified using cultures and PCR (polymerase chain reaction) with new research regarding a microbiota approach through 16S rRNA (16S ribosomal ribonucleic acid gene) or metagenomic analysis for selected carcinomas in the biliary tract.

Infection prevention and control research priorities: what do we need to combat healthcare-associated infections and antimicrobial resistance? Results of a narrative literature review and survey analysis

BACKGROUND

Infection prevention and control (IPC) is one of the most cost-effective interventions against antimicrobial resistance (AMR). Yet, IPC knowledge gaps often receive little prominence in AMR research agendas. In this article, we construct IPC research priorities, in order to draw attention to these critical research needs.

METHODS

We developed a 4-step framework to identify IPC knowledge gaps from literature (narrative review). These gaps were then translated into research priorities and sent to two groups of European IPC experts for validation and critique through an online survey.

RESULTS

Seventy-nine publications were retrieved from the literature review, identifying fifteen IPC research gaps. Forty-four IPC experts, clustered in two groups, vetted them. The experts classified all research gaps as medium or high priority. Overall agreement between both groups was average (Kendall's τ = 0.43), with strong alignment on the highest priorities: (i) the assessment of organizational, socio-economic, and behavioural barriers/facilitators for the implementation of IPC programmes, (ii) the impact of overcrowding on the spread of infections and (iii) the impact of infrastructural changes, at facility level, on the reduction of infections. Feedback from experts also identified an additional research gap on the interaction between the human and hospital microbiomes.

CONCLUSIONS

We formulated a list of sixteen research priorities and identified three urgent needs. Now, we encourage researchers, funding agencies, policymakers and relevant stakeholders to start addressing the identified gaps.

A randomized open label efficacy clinical trial of oral guava leaf decoction in patients with acute infectious diarrhoea

Background

Diarrhoea is amongst the first ten causes of death and its treatment faces an increased threat of drug resistance. Previous studies on the guava leaf decoction (GLD) revealed its suitability for use in infectious diarrhoea of unknown etiology.

Objective

The objective of this trial was to establish efficacy, dose and safety of GLD prepared from the Indian Sardar variety in adults with acute infectious diarrhoea.

Methods

The current trial was an open efficacy randomized 5-day, parallel group multi-arm interventional study. Amongst 137 adults (18–60 years) suffering with acute diarrhoea, 109 were included (57% females, 43% males). Three doses of GLD (6-leaf, 10-leaf and 14-leaf) were compared with controls receiving oral rehydration solution. Decrease in stool frequency and improvement in consistency were the outcomes measured. The data was analyzed using ANOVA, Tukey's post-hoc test, Kruscal-Wallis test and Chi-Square test where applicable.

Results

The trial showed that the 14-leaf (7.4 g) decoction was the most effective. Administration of the decoction, thrice daily helped the patients regain normalcy in 72 h as opposed to 120 h in controls. Safety of the intervention was reflected by normal levels of haemoglobin, liver and kidney parameters. No adverse events were reported.

Conclusion

The 14 leaves decoction was a safe treatment for adult acute uncomplicated diarrhoea of unknown etiology. Moreover due to component synergy and divergent mechanisms of action, it could possibly combat the generation of drug resistance and destruction of gut microbiota. Hence GLD has the potential for development as a first line treatment for diarrhoea.

Trial registration

Trial was registered with Clinical Trials Registry - India (CTRI registration number: CTRI/2016/07/007095). The trial was retrospectively registered.

Early-life sickness may predispose Siberian hamsters to behavioral changes following alterations of the gut microbiome in adulthood

Although it is well-established that the immune system plays an important role in the development of physiology and behavior, the gut microbiome has recently become of interest in the study of developmental origins of behavior. Studies suggest that the effects of early-life immune activation may not occur until a secondary stressor is introduced, though the precise nature and timing of the stressor may be critical in the response. Further, recent work suggests that the microbiome and the immune system develop in parallel, and therefore any perturbations to one of these systems early in life will likely affect the other. Here, we sought to determine whether early-life activation of the immune system had long-term consequences on how the gut microbiome responds to antibiotic treatment in adulthood and whether those changes influence adult same-sex social behavior. In order to test the hypothesis that an early-life immune challenge makes individuals more vulnerable to the effects of antibiotics, we mimicked an early-life infection by injecting pups at postnatal day 3 and 5 with lipopolysaccharide (LPS; cell wall component of gram-negative bacteria) or saline, and subsequently exposed the same animals to antibiotic treatment (known to influence microbial community composition and behavior) or water in adulthood. We tracked physiology across development, and paired males and females with a novel individual of the same age and sex in adulthood to score same-sex behavior (e.g., aggression, investigation, grooming) before antibiotic treatment, immediately following treatment, and after recovery from antibiotics. LPS-treated females exhibited impaired reproductive physiology and function in adulthood (e.g., smaller ovaries and abnormal estrous cycles), and female and male gut microbial communities were strongly affected by antibiotic treatment in adulthood, but only slightly affected by postnatal LPS alone. Interestingly, LPS-treated males exhibited more robust changes in their behavioral response following adult antibiotic treatment, including decreased investigation and increased grooming, suggestive of changes in anxiety-like behaviors. These data suggest that males may be more vulnerable than females to behavioral abnormalities after being predisposed to an immune challenge early in life. Collectively, these results provide novel evidence that some of the sex-specific behavioral consequences of an early-life immune challenge may not transpire until an individual is faced with a secondary challenge, and the context in which an individual is exposed can greatly influence the response.

Dual functional roles of the MyD88 signaling in colorectal cancer development

The myeloid differentiation factor 88 (MyD88), an adaptor protein in regulation of the innate immunity, functions to regulate immune responses against viral and bacterial infections in the human body. Toll-like receptors (TLRs) and interleukin 1 receptors (IL-1R) can recognize microbes or endogenous ligands and then recruit MyD88 to activate the MyD88-dependent pathway, while MyD88 mutation associated with lymphoma development and altered MyD88 signaling also involved in cancer-associated cell intrinsic and extrinsic inflammation progression and carcinogenesis. Detection of MyD88 expression was to predict prognosis of various human cancers, e.g., lymphoid, liver, and colorectal cancers. In human cancers, MyD88 protein acts as a bridge between the inflammatory signaling from the TLR/IL-1R and Ras oncogenic signaling pathway. However, the MyD88 signaling played dual functional roles in colorectal cancer, i.e., the tumor-promoting role that enhances cancer inflammation and intestinal flora imbalance to induce tumor invasion and tumor cell self-renewal, and the anti-tumor role that helps to maintain the host-microbiota homeostasis to induce tumor cell cycle arrest and immune responses against cancer cells. This review precisely discusses the up to date literature for these contrasting effects of MyD88 signaling on colorectal cancer development and progression.

Effect of Early Weaning on the Intestinal Microbiota and Expression of Genes Related to Barrier Function in Lambs

Weaning stress has been reported to impair intestinal health. The gut microbiota plays a vital role in the long-term health of the host. However, our understanding of weaning stress on gut microbiota and barrier function is very limited in livestock species, especially lambs. We investigated the effects of early weaning stress on intestinal bacterial communities and intestinal barrier function in lambs. A total of 24 neonatal male Hu lambs were randomly allocated into two groups, one weaned on day 28 and the other weaned on day 56. At 42 and 84 days, six lambs from each group were randomly selected and sacrificed. Ileal tissue and ileal digesta were collected to compare the differences in ileal microbiota and the mRNA levels of Toll-like receptors (TLRs) and tight junction proteins between the early weaning group and the control group at day 42 when the early weaning group have been weaned for 14 days, and at day 84 when the 28 and 56 days weaning groups had been weaned for 56 and 28 days, respectively. 16S rRNA gene sequencing of ileal samples revealed that the ileal microbiota was very different between the two groups, even at 84 days of age. Early weaning significantly increased alpha diversity and altered the relative abundance of several bacterial taxa. The expression of genes related to intestinal barrier function was affected by early weaning. Early weaning significantly increased ileal mRNA levels of TLR1 on days 42 and 84; TLR2, TLR4, and TLR5 on day 84; claudin1 and claudin4 on day 42; and occludin on day 84. We demonstrate that early weaning not only altered the ileal microbiota on day 42 (compared with lambs that were not weaned), but also had lasting effects on the ileal microbiota at day 84; furthermore, early weaning impacts expression levels of genes related to intestinal barrier function.

Guanosine tetra- and pentaphosphate increase antibiotic tolerance by reducing reactive oxygen species production in Vibrio cholerae

The pathogen Vibrio cholerae is the causative agent of cholera. Emergence of antibiotic-resistant V. cholerae strains is increasing, but the underlying mechanisms remain unclear. Herein, we report that the stringent response regulator and stress alarmone guanosine tetra- and pentaphosphate ((p)ppGpp) significantly contributes to antibiotic tolerance in V. cholerae We found that N16961, a pandemic V. cholerae strain, and its isogenic (p)ppGpp-overexpressing mutant ΔrelAΔspoT are both more antibiotic-resistant than (p)ppGpp⁰ (ΔrelAΔrelVΔspoT) and ΔdksA mutants, which cannot produce or utilize (p)ppGpp, respectively. We also found that additional disruption of the aconitase B-encoding and tricarboxylic acid (TCA) cycle gene acnB in the (p)ppGpp⁰ mutant increases its antibiotic tolerance. Moreover, expression of TCA cycle genes, including acnB, was increased in (p)ppGpp⁰, but not in the antibiotic-resistant ΔrelAΔspoT mutant, suggesting that (p)ppGpp suppresses TCA cycle activity, thereby entailing antibiotic resistance. Importantly, when grown anaerobically or incubated with an iron chelator, the (p)ppGpp⁰ mutant became antibiotic-tolerant, suggesting that reactive oxygen species (ROS) are involved in antibiotic-mediated bacterial killing. Consistent with that hypothesis, tetracycline treatment markedly increased ROS production in the antibiotic-susceptible mutants. Interestingly, expression of the Fe(III) ABC transporter substrate-binding protein FbpA was increased 10-fold in (p)ppGpp⁰, and fbpA gene deletion restored viability of tetracycline-exposed (p)ppGpp⁰ cells. Of note, FbpA expression was repressed in the (p)ppGpp-accumulating mutant, resulting in a reduction of intracellular free iron, required for the ROS-generating Fenton reaction. Our results indicate that (p)ppGpp-mediated suppression of central metabolism and iron uptake reduces antibiotic-induced oxidative stress in V. cholerae.

A single gene of a commensal microbe affects host susceptibility to enteric infection

Indigenous microbes inside the host intestine maintain a complex self-regulating community. The mechanisms by which gut microbes interact with intestinal pathogens remain largely unknown. Here we identify a commensal Escherichia coli strain whose expansion predisposes mice to infection by Vibrio cholerae, a human pathogen. We refer to this strain as ‘atypical’ E. coli (atEc) because of its inability to ferment lactose. The atEc strain is resistant to reactive oxygen species (ROS) and proliferates extensively in antibiotic-treated adult mice. V. cholerae infection is more severe in neonatal mice transplanted with atEc compared with those transplanted with a typical E. coli strain. Intestinal ROS levels are decreased in atEc-transplanted mice, favouring proliferation of ROS-sensitive V. cholerae. An atEc mutant defective in ROS degradation fails to facilitate V. cholerae infection when transplanted, suggesting that host infection susceptibility can be regulated by a single gene product of one particular commensal species.

The interactions between gut bacteria and enteric pathogens are poorly understood. Here, Yoon et al. show that subinhibitory antibiotic treatment in a mouse model leads to overgrowth of an E. coli strain carrying a catalase-encoding gene that enhances infection with the human pathogen Vibrio cholerae.

The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance

PURPOSE

Hospital-acquired infections are increasing in frequency due to multidrug resistant organisms (MDROs), and the spread of MDROs has eroded our ability to treat infections. Health care professionals cannot rely solely on traditional infection control measures and antimicrobial stewardship to prevent MDRO transmission. We review research on the microbiota as a target for infection control interventions.

METHODS

We performed a literature review of key research findings related to the microbiota as a target for infection control interventions. These data are summarized and used to outline challenges, opportunities, and unanswered questions in the field.

RESULTS

The healthy microbiota provides protective functions including colonization resistance, which refers to the microbiota's ability to prevent colonization and/or expansion of pathogens. Antibiotic use and other exposures in hospitalized patients are associated with disruptions of the microbiota that may reduce colonization resistance and select for antibiotic resistance. Novel methods to exploit protective mechanisms provided by an intact microbiota may provide the key to preventing the spread of MDROs in the health care setting.

CONCLUSIONS

Research on the microbiota as a target for infection control has been limited. Epidemiologic studies will facilitate progress toward the goal of manipulating the microbiota for control of MDROs in the health care setting.

(p)ppGpp, a Small Nucleotide Regulator, Directs the Metabolic Fate of Glucose in Vibrio cholerae

When V. cholerae encounters nutritional stress, it activates (p)ppGpp-mediated stringent response. The genes relA and relV are involved in the production of (p)ppGpp, whereas the spoT gene encodes an enzyme that hydrolyzes it. Herein, we show that the bacterial capability to produce (p)ppGpp plays an essential role in glucose metabolism. The V. cholerae mutants defective in (p)ppGpp production (i.e. ΔrelAΔrelV and ΔrelAΔrelVΔspoT mutants) lost their viability because of uncontrolled production of organic acids, when grown with extra glucose. In contrast, the ΔrelAΔspoT mutant, a (p)ppGpp overproducer strain, exhibited better growth in the presence of the same glucose concentration. An RNA sequencing analysis demonstrated that transcriptions of genes consisting of an operon for acetoin biosynthesis were markedly elevated in N16961, a seventh pandemic O1 strain, but not in its (p)ppGpp(0) mutant during glucose-stimulated growth. Transposon insertion in acetoin biosynthesis gene cluster resulted in glucose-induced loss of viability of the ΔrelAΔspoT mutant, further suggesting the crucial role of acetoin production in balanced growth under glucose-rich environments. Additional deletion of the aphA gene, encoding a negative regulator for acetoin production, failed to rescue the (p)ppGpp(0) mutant from the defective glucose-mediated growth, suggesting that (p)ppGpp-mediated acetoin production occurs independent of the presence of AphA. Overall, our results reveal that (p)ppGpp, in addition to its well known role as a stringent response mediator, positively regulates acetoin production that contributes to the successful glucose metabolism and consequently the proliferation of V. cholerae cells under a glucose-rich environment, a condition that may mimic the human intestine.