• barrier
• gastroesophageal reflux disease
• inflammation
• microbial dysbiosis
• microbiome
• motility

• Humans
• Gastroesophageal Reflux/microbiology
• Gastroesophageal Reflux/immunology
• Gastroesophageal Reflux/etiology
• Gastroesophageal Reflux/metabolism
• Gastrointestinal Microbiome/immunology
• Animals
• Dysbiosis/immunology
• Esophagus/microbiology
• Esophagus/immunology

• Microbiome
• breast milk expression
• breast pumping
• child development
• child health

• Humans
• Gastrointestinal Microbiome/physiology
• Infant
• Prospective Studies
• Breast Feeding
• Female
• Hong Kong
• Male
• Feces/microbiology
• Infant Formula
• Milk, Human/microbiology
• Infant, Newborn
• East Asian People

• Gastrointestinal cancers
• Metabolic interplay
• Microbiome
• Microbiome research
• Precision diagnosis
• Therapeutic approaches

• Mendelian randomization analysis
• causal relationship
• gastrointestinal microbiome
• systematic review
• thyroid neoplasms

• Humans
• Gastrointestinal Microbiome
• Genome-Wide Association Study
• Microbiota
• Thyroid Neoplasms/genetics

• 81930021 National Natural Science Foundation of China
• SHDC2020CR1001A Clinical Research Plan of SHDC
• 20152508 Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant Support

• Germ-free animal
• Microbial model
• Microbiota-directed foods and drugs
• Precision nutrition
• Simulated cultivation
• Specific physiological characteristics

• Gastrointestinal Microbiome
• Diet
• Microbiota
• Dietary Supplements
• Drug Design

• Clostridium butyricum
• Immunity
• Intestinal microorganisms
• Penaeus vannamei
• Vibrio alginolyticus

The intestinal dysfunction induced by high plant protein diets is frequently observed in farmed fish, and probiotics of Bacillus genus were documented to benefit the intestinal health through the modulation of intestinal microbiota without clearness in its underlying mechanism yet. Fusobacteria, Proteobacteria, and Firmicutes were observed to be the dominate phyla, but their proportion differentiated in the intestinal bacterial community of Pengze crucian carp (Carassius auratus var. Pengze) fed different diets in this study. Dietary supplementation of B. cereus and B. subtilis could reshape the intestinal bacterial community altered by high plant protein diets through a notable reduction in opportunistic pathogen Aeromonas together with an increase in Romboutsia and/or Clostridium_sensu_stricto from Firmicutes. Due to the alteration in the composition of bacterial community, Pengze crucian carp exhibited characteristic ecological networks dominated by cooperative interactions. Nevertheless, the increase in Aeromonas intensified the competition within bacterial communities and reduced the number of specialists within ecological network, contributing to the microbial dysbiosis induced by high plant protein diets. Two probiotics diets promoted the cooperation within the intestinal bacterial community and increased the number of specialists preferred to module hubs, and then further improved the homeostasis of the intestinal microbiota. Microbial dysbiosis lead to microbial dysfunction, and microbial lipopolysaccharide biosynthesis was observed to be elevated in high plant protein diets due to the increase in Aeromonas, gram-negative microbe. Probiotics B. cereus and B. subtilis restored the microbial function by elevating their amino acid and carbohydrate metabolism together with the promotion in the synthesis of primary and secondary bile acids. These results suggested that dietary supplementation of probiotics B. cereus and B. subtilis could restore the homeostasis and functions of intestinal microbiota in Pengze crucian carp fed high plant protein diets.

• Gut dysbiosis
• Gut microbial composition
• Maternal-to-infant transfer

• breastfeeding
• colonization
• delivery
• dysbiosis
• metagenomics
• microbiome
• neonatal microbiota
• womb sterile

Long-term antibiotic use can have consequences on systemic diseases, such as obesity, allergy, and depression, implicating the causal role of gut microbiome imbalance. However, the evaluation of the effect of antibiotics in early infancy on alterations to the gut microbiome remains poorly understood. This study aimed to evaluate the gut microbiome state in infancy following systemic antibiotic treatment. Twenty infants under 3 months of age who had received antibiotics for at least 3 days were enrolled, and their fecal samples were collected 4 weeks after antibiotic administration finished. Thirty-four age-matched healthy controls without prior exposure to antibiotics were also assessed. The relative bacterial abundance in feces was obtained via sequencing of 16 S rRNA genes, and alpha and beta diversities were evaluated. At the genus level, the relative abundance of Escherichia/Shigella and Bifidobacterium increased (p = 0.03 and p = 0.017, respectively) but that of Bacteroides decreased (p = 0.02) in the antibiotic treatment group. The microbiome of the antibiotic treatment group exhibited an alpha diversity lower than that of the control group. Thus, systemic antibiotic administration in early infancy affects the gut microbiome composition even after a month has passed; long-term studies are needed to further evaluate this.

• Gut microbiota
• androgen
• estrogen
• insulin
• reproductive endocrine

• diarrhea
• gastrointestinal parasites
• medical ward
• nosocomial infections

• gut microbiota (GM)
• human health
• interplay
• nutrition
• plant miRNAs

• Gastrointestinal Microbiome
• Gene Expression Regulation, Plant
• Humans
• MicroRNAs/genetics
• Plant Development
• Plants/genetics
• RNA, Plant/genetics

Bi-directional interactions amongst the gut microbiota, immune system, and brain function are thought to be critical mediators of health and disease. The role sleep plays in mediating these interactions is not known. We assessed the effects of sleep fragmentation (SF) on the microbiota–gut–brain axis. Male C57BL/6NCrl mice (4 to 5 per cage, fed standard lab chow) experienced SF via mechanical stimulation at 2 min intervals during the light (SF) and dark (DD, dark disturbances) periods. Home cage (HC) controls were undisturbed. After 10 days, fecal samples were collected at light onset, midday, light offset, and midnight. Samples were also collected after 10 days without SF. Subsequently, the mice were randomized across groups and allowed 20 additional days of recovery followed by 10 days of SF or DD. To assess effects on the microbiota, 16S rRNA sequencing was used, and mesenteric lymph nodes (MLNs) and cortex and medial prefrontal cortex were analyzed using cytokine arrays. SF and DD produced significant alterations in the microbiota compared to HC, and DD had greater impact than SF on some organisms. SF produced marked suppression in MLNs of chemokines that regulate inflammation (CCL3, CCL4 and their receptor CCR5) and maintain the immune mucosal barrier (Cxcl13) at the same time that cortical cytokines (IL-33) indicated neuroinflammation. DD effects on immune responses were similar to HC. These data suggest that SF alters the microbiome and suppresses mucosal immunity at the same time that mediators of brain inflammation are upregulated. The translational implications for potential application to clinical care are compelling.

• chemokine
• cytokine
• immune system
• microbiome
• neuroinflammation

• Antibiotic resistance genes
• Fungi
• Multitrophic communities
• Network analysis
• Neutral model
• Protist

• Animals
• Anti-Bacterial Agents
• Female
• Fungi/classification
• Gastrointestinal Microbiome
• Genes, Bacterial
• Male
• Microbiota
• Ursidae

• Graves’ disease
• Gut microbiota
• Lactobacillus
• Ruminococcus
• TRAb

• Adult
• Antithyroid Agents/therapeutic use
• Asian People
• Feces/microbiology
• Female
• Gastrointestinal Microbiome
• Graves Disease/genetics
• Graves Disease/microbiology
• Graves Disease/physiopathology
• Healthy Volunteers
• High-Throughput Nucleotide Sequencing
• Humans
• Lactobacillus
• Male
• Methimazole/therapeutic use
• Receptors, Thyrotropin/immunology
• Ruminococcus
• Thyroid Function Tests
• Young Adult

• BE2020701 Key Research and Development Plan Project of Jiangsu Province - Social Development Projects
• 81774134 National Natural Science Foundation of China
• 81873174 National Natural Science Foundation of China
• BK20150558 Natural Science Foundation of Jiangsu Province (CN)
• BK20171331 Natural Science Foundation of Jiangsu Province
• 1501120C Postdoctoral Science Foundation of Jiangsu Province
• BRA2017595 Jiangsu Province 333 Talent Funding Project
• QNRC2016902 Young Medical Key Talents Project of Jiangsu Province

• Biological effects
• Biosecurity
• Food
• Nanoparticles
• Toxicity

• Containment of Biohazards
• Food
• Nanoparticles/toxicity
• Nanotechnology
• Risk Assessment

• Antibiotic growth promoter
• Guinea pig
• Probiotics
• Productive parameters

• Animal Feed/analysis
• Animals
• Guinea Pigs
• Lactobacillus
• Male
• Probiotics/pharmacology
• Streptococcus

• antibiotics
• bifidobacteria
• comparative genomics

Obesity is a major public health problem that continues to be one of the leading risk factors for premature death. Early life is a critical period of time when the gut microbiota and host metabolism are developing in tandem and significantly contribute to long-term health outcomes. Dysbiosis of the gut microbiota, particularly in early life, can have detrimental effects on host health and increase the susceptibility of developing obesity later in life. Antibiotics are an essential lifesaving treatment; however, their use in early life may not be without risk. Antibiotics are a leading cause of intestinal dysbiosis, and early life administration is associated with obesity risk. The following review explores the relevant literature that simultaneously examines antibiotic-induced dysbiosis and obesity risk. Current evidence suggests that disruptions to the composition and maturation of the gut microbiota caused by antibiotic use in early life are a key mechanism linking the association between antibiotics and obesity. Without compromising clinical practice, increased consideration of the long-term adverse effects of antibiotic treatment on host health, particularly when used in early life is warranted. Novel adjunct interventions should be investigated (e.g., prebiotics) to help mitigate metabolic risk when antibiotic treatment is clinically necessary.

• antibiotics
• early-life
• gut microbiota
• infancy
• obesity risk

• Antibiotic alternatives
• Broilers
• Cyclic heat stress
• Growth
• Humoral immunity
• Microflora

• gut
• microbiota
• pre-diabetes
• type 2 diabetes

• National Institute for Medical Research Development

• asthma
• caesarean section
• neonatal outcomes
• neurological disorders
• obesity
• overweight
• respiratory disorders

• Asthma/epidemiology
• Cesarean Section/adverse effects
• Child
• Cohort Studies
• Female
• Humans
• Obesity/epidemiology
• Pediatrics
• Pregnancy
• Prospective Studies
• Respiratory Tract Diseases/epidemiology
• Retrospective Studies
• Risk Factors

• Akkermansia muciniphila
• Th1- & Th2-biased mice
• cecal microbiota transplantation
• gut microbiota
• vancomycin

• MEFV
• amyloidosis
• colchicine
• inflammasome
• interleukin-1b

• Environment
• Familial Mediterranean Fever/genetics
• Familial Mediterranean Fever/microbiology
• Familial Mediterranean Fever/pathology
• Gastrointestinal Microbiome
• Genetic Background
• Humans

• R01 DK106249 NIDDK NIH HHS
• R01 DK114516 NIDDK NIH HHS
• R01 DK126369 NIDDK NIH HHS

Microbial colonisation of the gastrointestinal tract of newly hatched chicks starts at hatch, seeded from the immediate hatching environment, and quickly results in dense colonisation. The role of ecological factors in gut colonisation has been extensively investigated, as well as the role of micro- and macronutrients in supporting and selecting for bacterial species highly adapted for utilising those nutrients. However, the microbial community contained in poultry feed and its influence on colonisation and maturation of gut microbiota has not been directly addressed. In this study, we compared the microbiota found in poultry feed, with the microbiota of ileum, cecum and excreta, to identify substantial overlap in core microbiotas of the compared groups. We then investigated the microbiota present in raw feedstuffs: meat and bone meal, wheat, corn, canola, barley, soybean, millrun, sorghum, poultry oil, oats, limestone and bloodmeal from four geographically distinct feedstuff suppliers. Each of the feedstuffs had diverse microbial communities. The meat and bone meal and bloodmeal samples had the most complex and distinct microbial populations. There was substantial overlap in the phylogenetic composition found in the grain and seed samples: barley, canola, corn, millrun, oats, sorghum, soybean meal and wheat. Issues related to methodology, viability of microbial communities in the gut and feed, and the implications for biosecurity are discussed.

• Chicken
• Colonisation
• Feed
• Microbiota

• PCNA-ir cells
• antioxidant enzymes
• gastrointestinal toxicity
• genotoxicity
• histopathological architecture
• hydroxyapatite nanoparticles
• immunohistochemistry
• nano-antioxidants
• oxidative DNA damage
• oxidative stress
• proinflammatory cytokines

• Firmicutes
• corn
• dietary miRNAs
• gut microbiota
• plant

• U.S. Department of Agriculture
• Office of Dietary Supplements

• Bacteroides spp.
• Cholesterol homeostasis
• Gut microbiota
• Niemann-pick C1-like 1
• Outer membrane vesicles (OMVs)

• asthma
• developmental disabilities
• gastrointestinal microbiome
• human milk
• infant formula
• microbiota
• obesity
• pediatrics
• prebiotics

• Bifidobacterium bifidum
• Cervical cancer
• Human papillomavirus
• IL-6
• Immune response
• Probiotics

The epithelial barrier in the gastrointestinal (GI) tract is a protective interface that endures constant exposure to the external environment while maintaining its close contact with the local immune system. Growing evidence has suggested that the intercellular crosstalk in the GI tract contributes to maintaining the homeostasis in coordination with the intestinal microbiome as well as the tissue-specific local immune elements. Thus, it is critical to map the complex crosstalks in the intestinal epithelial-microbiome-immune (EMI) axis to identify a pathological trigger in the development of intestinal inflammation, including inflammatory bowel disease. However, deciphering a specific contributor to the onset of pathophysiological cascades has been considerably hindered by the challenges in current in vivo and in vitro models. Here, we introduce various microphysiological engineering models of human immune responses in the EMI axis under the healthy conditions and gut inflammation. As a prospective model, we highlight how the human “gut inflammation-on-a-chip” can reconstitute the pathophysiological immune responses and contribute to understanding the independent role of inflammatory factors in the EMI axis on the initiation of immune responses under barrier dysfunction. We envision that the microengineered immune models can be useful to build a customizable patient's chip for the advance in precision medicine.

• Co-culture
• Gut inflammation-on-a-chip
• Immune response
• Microbiome
• Microphysiological system
• Organoid

• 16S ribosomal RNA gene sequencing
• Childhood nutrition
• Dietary composition
• Fortified grains
• Gut microbiome

• Child
• Child Nutritional Physiological Phenomena
• Child, Preschool
• Cross-Sectional Studies
• Diet/methods
• Diet/statistics & numerical data
• Diet Surveys
• Eating/physiology
• Feces/microbiology
• Feeding Behavior/physiology
• Female
• Gastrointestinal Microbiome
• Humans
• Male
• RNA, Ribosomal, 16S/analysis
• United States

• RL5 GM118975 NIGMS NIH HHS
• T32 AI141346 NIAID NIH HHS
• UL1 GM118976 NIGMS NIH HHS

• QIIME
• microbiome
• pathobiome
• sub-Saharan Africa
• taxonomy

• administration, rectal
• hypothermia, induced
• hypoxia-ischemia, brain

• Amine Oxidase (Copper-Containing)/metabolism
• Animals
• Bacteria/isolation & purification
• Bacterial Translocation
• Hypothermia, Induced
• Hypoxia-Ischemia, Brain/microbiology
• Hypoxia-Ischemia, Brain/therapy
• Inflammation/blood
• Inflammation/pathology
• Intestines/microbiology
• Lactic Acid/blood
• Male
• Rats, Sprague-Dawley
• Rectum/pathology

• Adolescents
• Inflammatory bowel disease
• Microbiome
• Vitamin D

• Adolescent
• Bacteria/classification
• Child
• Cohort Studies
• DNA, Bacterial
• Feces/microbiology
• Female
• Gastrointestinal Microbiome/drug effects
• Gastrointestinal Tract/microbiology
• Humans
• Inflammatory Bowel Diseases
• Vitamin D/pharmacology
• Vitamin D Deficiency

• Bifidobacteria
• Immune response
• Microbiome
• Multiple sclerosis

• Diet, Vegan
• Diet, Vegetarian
• Drug Resistance, Microbial
• Erythromycin/pharmacology
• Gastrointestinal Microbiome
• Humans
• Lactobacillales/drug effects
• Lactobacillales/isolation & purification
• Vegans
• Vegetarians

• Italian Ministry of University and Research

• Graves’ disease
• Hashimoto’s thyroiditis
• autoimmune disease
• dysbiosis
• enterohepatic cycling of thyroid hormones
• probiotics

• Animals
• Graves Disease/metabolism
• Hashimoto Disease/metabolism
• Humans
• Microbiota/physiology
• Probiotics
• Thyroid Gland/metabolism
• Thyroid Hormones/metabolism

Ecological relationships between bacteria are important when considering variation in bacterial communities in humans, with such variation playing an important role in both health and disease.

Using high-throughput sequence data of the 16S rRNA marker-gene, we analysed the prevalence of taxa in the airways of a number of health- and disease-associated cohorts and determined the main drivers of community variance and bacterial co-occurrence.

A number of facultative and obligately anaerobic bacterial taxa are commonly associated with the upper airways, forming the main “core” microbiota, e.g. Streptococcus spp., Veillonella spp., Prevotella spp., Granulicatella spp. and Fusobacterium spp. Opportunistic pathogenic bacteria associated with chronic airways disease, such as Pseudomonas spp. (Pseudomonas aeruginosa), Burkholderia spp. (Burkholderia cepacia complex) and Haemophilus spp. (Haemophilus influenzae) demonstrated poor correlation with other members of their respective communities (ρ<0.5; p>0.005), indicating probable independent acquisition and colonisation. Furthermore, our findings suggest that intra-genus variation between health and disease may affect community assemblies.

Improved understanding of how bacteria assemble in time and space during health and disease will enable the future development of tailored treatment according to the patient's own signature microbiota, potentially providing benefit to patients suffering from airway diseases characterised by chronic infection.

Within the airways, “core” community structures are formed between microbial taxa in both health and disease, with a number of common opportunistic pathogens not being members of such core communitieshttp://bit.ly/2Kau3ni

• cecal microbiota
• gut health
• rabbit
• water temperature
• welfare
• winter

• ARS-43-D-1 China Agriculture Research System for Rabbits
• No. 201303145 Specific Funds of Public Service Research

• Chemical mixtures
• Environmental pollutants
• Gut microbiota
• Host health
• Toxicity

• Environmental Pollutants/toxicity
• Gastrointestinal Microbiome/drug effects
• Hazardous Substances/toxicity
• Humans

MNGIE is a rare and fatal disease in which absence of the enzyme thymidine phosphorylase induces systemic accumulation of thymidine and deoxyuridine and secondary mitochondrial DNA alterations. Gastrointestinal (GI) symptoms are frequently reported in MNGIE patients, however, they are not resolved with the current treatment interventions.

Recently, our understanding of the GI pathology has increased, which rationalizes the pursuit of more targeted therapeutic strategies. In particular, interstitial cells of Cajal (ICC) play key roles in GI physiology and are involved in the pathogenesis of the GI dysmotility. However, understanding of the triggers of ICC deficits in MNGIE is lacking. Herein, we review the current knowledge about the pathology of GI dysmotility in MNGIE, discuss potential mechanisms in relation to ICC loss/dysfunction, remark on the limited contribution of the current treatments, and propose intervention strategies to overcome ICC deficits. Finally, we address the advances and new research avenues offered by organoids and tissue engineering technologies, and propose schemes to implement to further our understanding of the GI pathology and utility in regenerative and personalized medicine in MNGIE.

Interstitial cells of Cajal play key roles in the physiology of the gastrointestinal motility. Evaluation of their status in the GI dysmotility related to MNGIE would be valuable for diagnosis of MNGIE. Understanding the underlying pathological and molecular mechanisms affecting ICC is an asset for the development of targeted prevention and treatment strategies for the GI dysmotility related to MNGIE.

• CIPO
• Chronic intestinal pseudo-obstruction
• HSCT
• ICC
• Interstitial cells of Cajal
• Intestinal organoids
• MNGIE
• Mitochondrial neurogastrointestinal encephalomyopathy