• 16S analysis
• dairy cattle
• fecal microbiota
• whole genome-wide association study

• Helper T cells
• Intestinal flora
• Pre-clinical
• Prevention
• Rheumatoid arthritis
• Risk factor

• alcohol
• bacteria
• fungi
• laryngeal squamous cell carcinoma
• recurrence

• Mycobiome
• Humans
• Laryngeal Neoplasms/microbiology
• Laryngeal Neoplasms/pathology
• Bacteria/classification
• Bacteria/genetics
• Bacteria/isolation & purification
• Male
• Middle Aged
• Female
• Carcinoma, Squamous Cell/microbiology
• Neoplasm Recurrence, Local/microbiology
• Fungi/classification
• Fungi/genetics
• Fungi/isolation & purification
• Aged
• Microbiota
• RNA, Ribosomal, 16S/genetics
• RNA, Ribosomal, 16S/analysis

• 82273097 MOST | National Natural Science Foundation of China (NSFC)
• 23ZR1409700 STCSM | Natural Science Foundation of Shanghai Municipality
• 22YF1405700 to CYH Shanghai Sailing Program
• 82203727 MOST | National Natural Science Foundation of China (NSFC)

• Clostridioides difficile
• Fecal microbiota transplantation
• Feces
• Gut microbiota
• Recurrent C. difficile infection

• Fecal Microbiota Transplantation/methods
• Humans
• Gastrointestinal Microbiome
• Clostridium Infections/therapy
• Clostridium Infections/microbiology
• Feces/microbiology
• Clostridioides difficile
• Dysbiosis/therapy
• Dysbiosis/microbiology
• Animals

• RS-2024-00340833 National Research Foundation of Korea

• gut barrier
• gut microbes
• intestinal permeability
• leaky gut
• microbiome

• COPD
• Live microbe
• NHANES
• Prevalence

• Humans
• Pulmonary Disease, Chronic Obstructive/epidemiology
• Cross-Sectional Studies
• Female
• Male
• Middle Aged
• Adult
• Prevalence
• Nutrition Surveys
• Diet/statistics & numerical data
• Aged
• Logistic Models
• United States/epidemiology
• Risk Factors
• Young Adult
• Smoking/epidemiology

• 2021KFJJ09 Special Fund for Rehabilitation Medicine of National Clinical Research Center for Geriatric Disorders Clinical Research Fund of Xiangya hospital
• 2021KFJJ09 Special Fund for Rehabilitation Medicine of National Clinical Research Center for Geriatric Disorders Clinical Research Fund of Xiangya hospital
• 2021KFJJ09 Special Fund for Rehabilitation Medicine of National Clinical Research Center for Geriatric Disorders Clinical Research Fund of Xiangya hospital

• colorectal cancer
• intestinal immunity
• intestinal microbiota
• metabolites
• postbiotics

• Malignancies
• Meta-analysis
• Oral microbiome
• Survival

• Humans
• Prognosis
• Neoplasms
• Disease-Free Survival
• Microbiota

• P30 CA054174 NCI NIH HHS
• R01 AI143313 NIAID NIH HHS
• S10 OD030432 NIH HHS

• donkey foal
• gut microbes
• metabolome
• serum
• weaning

• Microbiome
• bone health
• gut-bone axis
• musculoskeletal disease
• musculoskeletal health

• Humans
• Gastrointestinal Microbiome/physiology
• Bone and Bones/microbiology
• Musculoskeletal Diseases/microbiology
• Musculoskeletal Diseases/physiopathology
• Animals
• Osteoarthritis/microbiology
• Osteoarthritis/therapy
• Osteoporosis/microbiology
• Bone Density
• Musculoskeletal System/microbiology

• Crohn’s disease
• Inflammatory bowel disease
• MAIT cell
• Ulcerative colitis

• Animals
• Humans
• Mucosal-Associated Invariant T Cells/pathology
• Inflammatory Bowel Diseases/pathology
• Cytokines
• Biomarkers
• Receptors, Antigen, T-Cell, alpha-beta

• PW2021A-25 Project of Shanghai New District Health Commission

• Case–control study
• Fungi
• ITS sequencing
• Microbiome
• Nasopharyngeal carcinoma
• Oral mycobiome

• Humans
• Nasopharyngeal Carcinoma
• Dysbiosis
• Case-Control Studies
• Mycobiome
• Saccharomyces cerevisiae
• Nasopharyngeal Neoplasms/epidemiology
• Nasopharyngeal Neoplasms/complications

• R01 CA115873 NCI NIH HHS

• anti-inflammatory
• bioactive compounds
• colorectal cancer (CRC)
• gut microbiota
• gut microbiota–brain axis GMBA
• inflammation
• inflammatory bowel disease (IBD)
• inflammatory mediators

• RA
• dysbiosis
• intestinal
• microbiome
• pathogenesis

• biliary tract cancer
• cholangiocarcinoma
• gut-liver axis
• microbiota

• Humans
• Bile Duct Neoplasms/pathology
• Cholangiocarcinoma/pathology
• Carcinogenesis/pathology
• Microbiota
• Bile Ducts, Intrahepatic/pathology
• Tumor Microenvironment

• COVID-19
• Gut-lung axis
• immune modulation
• lung dysbiosis
• microbiome-based therapeutics

The human gut possesses millions of microbes that define a complex microbial community. The gut microbiota has been characterized as a vital organ forming its multidirectional connecting axis with other organs. This gut microbiota axis is responsible for host-microbe interactions and works by communicating with the neural, endocrinal, humoral, immunological, and metabolic pathways. The human gut microorganisms (mostly non-pathogenic) have symbiotic host relationships and are usually associated with the host’s immunity to defend against pathogenic invasion. The dysbiosis of the gut microbiota is therefore linked to various human diseases, such as anxiety, depression, hypertension, cardiovascular diseases, obesity, diabetes, inflammatory bowel disease, and cancer. The mechanism leading to the disease development has a crucial correlation with gut microbiota, metabolic products, and host immune response in humans. The understanding of mechanisms over gut microbiota exerts its positive or harmful impacts remains largely undefined. However, many recent clinical studies conducted worldwide are demonstrating the relation of specific microbial species and eubiosis in health and disease. A comprehensive understanding of gut microbiota interactions, its role in health and disease, and recent updates on the subject are the striking topics of the current review. We have also addressed the daunting challenges that must be brought under control to maintain health and treat diseases.

• COVID-19
• Children
• Dysbiosis
• Gut
• Microbiome
• Microbiota

The gut barrier is a single cell layer that separates gut micro-organisms from the host, and gut permeability defects result in the translocation of microbial molecules from the gut into the blood. Despite the silent clinical manifestation, gut translocation of microbial molecules can induce systemic inflammation that might be an endogenous exacerbating factor of systemic lupus erythematosus. In contrast, circulatory immune-complex deposition and the effect of medications on the gut, an organ with an extremely large surface area, of patients with active lupus might cause gut translocation of microbial molecules, which worsens lupus severity. Likewise, the imbalance of gut microbiota may initiate lupus and/or interfere with gut integrity which results in microbial translocation and lupus exacerbation. Moreover, immune hyper-responsiveness of innate immune cells (macrophages and neutrophils) is demonstrated in a lupus model from the loss of inhibitory Fc gamma receptor IIb (FcgRIIb), which induces prominent responses through the cross-link between activating-FcgRs and innate immune receptors. The immune hyper-responsiveness can cause cell death, especially apoptosis and neutrophil extracellular traps (NETosis), which possibly exacerbates lupus, partly through the enhanced exposure of the self-antigens. Leaky gut monitoring and treatments (such as probiotics) might be beneficial in lupus. Here, we discuss the current information on leaky gut in lupus.

• innate immunity
• leaky gut
• systemic lupus erythematosus

• Autoimmune Diseases
• Humans
• Immunity, Innate
• Lupus Erythematosus, Systemic
• Macrophages/metabolism
• Neutrophils/metabolism

• Esophageal adenocarcinoma
• Esophageal squamous cell carcinoma
• Inflammation, Microbiome
• Tumor microenvironment

• Carcinogenesis
• Carcinoma, Squamous Cell/pathology
• Cell Transformation, Neoplastic
• Esophageal Neoplasms
• Humans
• Inflammation
• Microbiota
• Tumor Microenvironment

• Hamad Medical Corporation
• All-India Institute of Medical Sciences
• Sidra Medicine Precision Program

• SCFAs
• gut microbiota
• high-calorie diet
• pneumonia

The human microbiome has been reported to mediate the response to anticancer therapies. However, research about the influence of the oral microbiome on nasopharyngeal carcinoma (NPC) survival is lacking. We aimed to explore the effect of oral microbiota on NPC prognosis.

Four hundred eighty-two population-based NPC cases in southern China between 2010 and 2013 were followed for survival, and their saliva samples were profiled using 16s rRNA sequencing. We analyzed associations of the oral microbiome diversity with mortality from all causes and NPC.

Within- and between-community diversities of saliva were associated with mortality with an average of 5.29 years follow-up. Lower Faith’s phylogenetic diversity was related to higher all-cause mortality [adjusted hazard ratio (aHR), 1.52 (95% confidence interval (CI), 1.06–2.17)] and NPC-specific mortality [aHR, 1.57 (95% CI, 1.07–2.29)], compared with medium diversity, but higher phylogenetic diversity was not protective. The third principal coordinate (PC3) identified from principal coordinates analysis (PCoA) on Bray–Curtis distance was marginally associated with reduced all-cause mortality [aHR, 0.85 (95% CI, 0.73–1.00)], as was the first principal coordinate (PC1) from PCoA on weighted UniFrac [aHR, 0.86 (95% CI, 0.74–1.00)], but neither was associated with NPC-specific mortality. PC3 from robust principal components analysis was associated with lower all-cause and NPC-specific mortalities, with HRs of 0.72 (95% CI, 0.61–0.85) and 0.71 (95% CI, 0.60–0.85), respectively.

Oral microbiome may be an explanatory factor for NPC prognosis. Lower within-community diversity was associated with higher mortality, and certain measures of between-community diversity were related to mortality. Specifically, candidate bacteria were not related to mortality, suggesting that observed associations may be due to global patterns rather than particular pathogens.

• Humans
• Nasopharyngeal Carcinoma
• Nasopharyngeal Neoplasms/microbiology
• Phylogeny
• RNA, Ribosomal, 16S/genetics
• Saliva/microbiology

• National Cancer Institute
• Vårdalstiftelsen
• National Natural Science Foundation of China
• China Scholarship Council

Cattle production is one of the key contributors to global warming due to methane emission, which is a by-product of converting feed stuff into milk and meat for human consumption. Rumen hosts numerous microbial communities that are involved in the digestive process, leading to notable amounts of methane emission. The key factors underlying differences in methane emission between individual animals are due to, among other factors, both specific enrichments of certain microbial communities and host genetic factors that influence the microbial abundances. The detection of such factors involves various biostatistical and bioinformatics methods. In this study, our main objective was to reanalyze a publicly available data set using our proprietary Synomics Insights platform that is based on novel combinatorial network and machine learning methods to detect key metagenomic and host genetic features for methane emission and residual feed intake (RFI) in dairy cattle. The other objective was to compare the results with publicly available standard tools, such as those found in the microbiome bioinformatics platform QIIME2 and classic GWAS analysis. The data set used was publicly available and comprised 1,016 dairy cows with 16S short read sequencing data from two dairy cow breeds: Holstein and Nordic Reds. Host genomic data consisted of both 50 k and 150 k SNP arrays. Although several traits were analyzed by the original authors, here, we considered only methane emission as key phenotype for associating microbial communities and host genetic factors. The Synomics Insights platform is based on combinatorial methods that can identify taxa that are differentially abundant between animals showing high or low methane emission or RFI. Focusing exclusively on enriched taxa, for methane emission, the study identified 26 order-level taxa that combinatorial networks reported as significantly enriched either in high or low emitters. Additionally, a Z-test on proportions found 21/26 (81%) of these taxa were differentially enriched between high and low emitters (p value <.05). In particular, the phylum of Proteobacteria and the order Desulfovibrionales were found enriched in high emitters while the order Veillonellales was found to be more abundant in low emitters as previously reported for cattle (Wallace et al., 2015). In comparison, using the publicly available tool ANCOM only the order Methanosarcinales could be identified as differentially abundant between the two groups. We also investigated a link between host genome and rumen microbiome by applying our Synomics Insights platform and comparing it with an industry standard GWAS method. This resulted in the identification of genetic determinants in cows that are associated with changes in heritable components of the rumen microbiome. Only four key SNPs were found by both our platform and GWAS, whereas the Synomics Insights platform identified 1,290 significant SNPs that were not found by GWAS. Gene Ontology (GO) analysis found transcription factor as the dominant biological function. We estimated heritability of a core 73 taxa from the original set of 150 core order-level taxonomies and showed that some species are medium to highly heritable (0.25–0.62), paving the way for selective breeding of animals with desirable core microbiome characteristics. We identified a set of 113 key SNPs associated with >90% of these core heritable taxonomies. Finally, we have characterized a small set (<10) of SNPs strongly associated with key heritable bacterial orders with known role in methanogenesis, such as Desulfobacterales and Methanobacteriales.

• cattle
• combinatorial analyses
• heritability
• methane emission
• rumen microbiome
• synomics insight

• adverse events
• antibiotics
• cancer
• dysbiosis
• microbiota
• patient treatment outcomes
• radiation therapy
• radiation-induced toxicity
• radiosensitization

As the number of households that raise dogs and cats is increasing, there is growing interest in animal health. The gut plays an important role in animal health. In particular, the microbiome in the gut is known to affect both the absorption and metabolism of nutrients and the protective functions of the host. Using probiotics on pets has beneficial effects, such as modulating the immune system, helping to reduce stress, protecting against pathogenic bacteria and developing growth performance. The goals of this review are to summarize the relationship between probiotics/the gut microbiome and animal health, to feature technology used for identifying the diversity of microbiota composition of canine and feline microbiota, and to discuss recent reports on probiotics in canines and felines and the safety issues associated with probiotics and the gut microbiome in companion animals.

• National Research Foundation of Korea

• biomarker
• carcinogenesis
• esophageal cancer
• microbiota
• therapeutic complication

• autoimmune diseases
• immune homeostasis
• intestinal microbiota
• ocular disease

• Breast cancer
• Breast microbiome
• Dysbiosis
• Inflammation
• Metabolite
• Micronutrition
• Probiotics
• Transfer RNAs

• R01 DK105118 NIDDK NIH HHS
• R01 DK114126 NIDDK NIH HHS

• Gastrointestinal optimization
• Inflammatory bowel disease
• Microbiome
• Obesity
• Pancreatic cancer

• Crohn’s disease
• IBD
• LPS
• Th17
• Tregs
• inflammation
• metabolic endotoxemia
• microbiota
• ulcerative colitis

• Animals
• Gastrointestinal Microbiome
• Humans
• Immunity, Innate/immunology
• Inflammatory Bowel Diseases/etiology
• Inflammatory Bowel Diseases/pathology
• Lipopolysaccharides/pharmacology

• blood-brain barrier
• immune system
• microbiota-gut-brain axis
• neurodegenerative disorders
• organ-on-a-chip

• Bioengineering
• Communication
• Gastrointestinal Microbiome
• Humans
• Microbiota
• Neurodegenerative Diseases

• European Research Council
• H2020 European Research Council

Cancer immunotherapy has shifted the paradigm in cancer treatment in recent years. Immune checkpoint blockage (ICB), the active cancer vaccination and chimeric antigen receptor (CAR) for T-cell-based adoptive cell transfer represent the main developments, achieving a surprising increased survival in patients included in clinical trials. In spite of these results, the current state-of-the-art immunotherapy has its limitations in efficacy. The existence of an interdisciplinary interface involving current knowledge in biology, immunology, bioengineering and materials science represents important progress in increasing the effectiveness of immunotherapy in cancer. Cutaneous melanoma remains a difficult cancer to treat, in which immunotherapy is a major therapeutic option. In fact, enhancing immunotherapy is possible using sophisticated biomedical nanotechnology platforms of organic or inorganic materials or engineering various immune cells to enhance the immune system. In addition, biological devices have developed, changing the approach to and treatment results in melanoma. In this review, we present different modalities to modulate the immune system, as well as opportunities and challenges in melanoma treatment.

• cutaneous melanoma
• immunotherapy
• nano-agents
• nanomedicine
• nanotechnology

Intestinal mucus protects epithelial and immune cells from the gut resident microorganisms, and provides growth-promoting factors as mucus-derived O-glycans for beneficial bacteria. A lack of intestinal protective mucus results in changes in the commensal microflora composition, mucosal immune system reprogramming, and inflammation. Previous work has shown that fucose, the terminal glycan chain component of the intestinal glycoprotein Mucin2, and fucoidan polysaccharides have an anti-inflammatory effect in some mouse models of colitis. This study evaluates the effect of fucose on reproductive performance in heterozygous mutant Muc2 female mice. We found that even though Muc2^+/− females are physiologically indistinguishable from C57Bl/6 mice, they have a significantly reduced reproductive performance upon dietary fucose supplementation. Metagenomic analysis reveals that the otherwise healthy wild-type siblings of Muc2^−/− animals have reduced numbers of some of the intestinal commensal bacterial species, compared to C57BL/6 mice. We propose that the changes in beneficial microflora affect the immune status in Muc2^+/− mice, which causes implantation impairment. In accordance with this hypothesis, we find that macrophage polarization during pregnancy is impaired in Muc2^+/− females upon addition of fucose. Metabolic profiling of peritoneal macrophages from Muc2^+/− females reveals their predisposition towards anaerobic glycolysis in favor of oxidative phosphorylation, compared to C57BL/6-derived cells. In vitro experiments on phagocytosis activity and mitochondrial respiration suggest that fucose affects oxidative phosphorylation in a genotype-specific manner, which might interfere with implantation depending on the initial status of macrophages. This hypothesis is further confirmed in BALB/c female mice, where fucose caused pregnancy loss and opposed implantation-associated M2 macrophage polarization. Taken together, these data suggest that intestinal microflora affects host immunity and pregnancy outcome. At the same time, dietary fucose might act as a differential regulator of macrophage polarization during implantation, depending on the immune status of the host.

• Mucin 2
• embryo implantation
• fucose
• immune response
• macrophages
• pregnancy

The gut microbiota is a complex ecological community that plays multiple critical roles within a host. Known intrinsic and extrinsic factors affect gut microbiota structure, but the influence of host genetics is understudied. To investigate the role of host genetics upon the gut microbiota structure, we performed a longitudinal study in which we evaluated the hindgut microbiota and its association with animal growth and immunity across life. We evaluated three different growth stages in an Angus-Brahman multibreed population with a graduated spectrum of genetic variation, raised under variable environmental conditions and diets. We found the gut microbiota structure was changed significantly during growth when preweaning, and fattening calves experienced large variations in diet and environmental changes. However, regardless of the growth stage, we found gut microbiota is significantly influenced by breed composition throughout life. Host genetics explained the relative abundances of 52.2%, 40.0%, and 37.3% of core bacterial taxa at the genus level in preweaning, postweaning, and fattening calves, respectively. Sutterella, Oscillospira, and Roseburia were consistently associated with breed composition at these three growth stages. Especially, butyrate-producing bacteria, Roseburia and Oscillospira, were associated with nine single-nucleotide polymorphisms (SNPs) located in genes involved in the regulation of host immunity and metabolism in the hindgut. Furthermore, minor allele frequency analysis found breed-associated SNPs in the short-chain fatty acids (SCFAs) receptor genes that promote anti-inflammation and enhance intestinal epithelial barrier functions. Our findings provide evidence of dynamic and lifelong host genetic effects upon gut microbiota, regardless of growth stages. We propose that diet, environmental changes, and genetic components may explain observed variation in critical hindgut microbiota throughout life.

• fecal microbiome transplant
• gut microbiome
• human microbiome
• pathogenesis
• symbiosis

• Animals
• Bile/microbiology
• Bile Duct Neoplasms/immunology
• Bile Duct Neoplasms/microbiology
• Bile Duct Neoplasms/pathology
• Bile Ducts/immunology
• Bile Ducts/microbiology
• Bile Ducts/pathology
• Carcinogenesis/immunology
• Cholangiocarcinoma/immunology
• Cholangiocarcinoma/microbiology
• Cholangiocarcinoma/pathology
• Disease Models, Animal
• Dysbiosis/diagnosis
• Dysbiosis/immunology
• Dysbiosis/microbiology
• Feces/microbiology
• Gastrointestinal Microbiome/immunology
• Helicobacter/isolation & purification
• Humans
• Liver/immunology
• Liver/microbiology
• Liver/pathology
• Opisthorchiasis/complications
• Opisthorchiasis/diagnosis
• Opisthorchiasis/immunology
• Opisthorchiasis/parasitology
• Opisthorchis/immunology
• Opisthorchis/isolation & purification

Vaccinations are among the most effective medical procedures and have had an incredible impact on almost everyone’s life. One of the populations that can benefit the most from them are elderly people. Unfortunately, in this group, vaccines are less effective than in other groups, due to immunosenescence. The immune system ages like the whole body and becomes less effective in responding to infections and vaccinations. At the same time, immunosenescence also favors an inflammatory microenvironment, which is linked to many conditions typical of the geriatrics population. The microbiota is one of the key actors in modulating the immune response and, in this review, we discuss the current evidence on the role of microbiota in regulating the immune response to vaccines, particularly in elderly people.

• immunosenescence
• inflammaging
• microbiota
• vaccines

• COVID-19
• SARS-CoV-2
• children
• immunology
• novel coronavirus

• Anti-oxidative capacity
• Evidence-based medicine
• Food microbiology
• Gut microflora
• Immunity
• Lactobacillus paracasei subsp. paracasei NTU 101
• Microbiology
• Nutrition
• Probiotics