Why related bacterial species bloom simultaneously in the gut: principles underlying the 'Like will to like' concept

Harnessing the fish gut microbiome and immune system to enhance disease resistance in aquaculture

The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.

Physiological and intestinal microbiota responses of sea cucumber Apostichopus japonicus to various stress and signatures of intestinal microbiota dysbiosis

Identifying the signatures of intestinal dysbiosis caused by common stresses is fundamental to establishing efficient health monitoring strategies for sea cucumber. This study investigated the impact of six common stress experienced frequently in aquaculture on the growth performance, intestinal homeostasis and microbiota of sea cucumber, including thermal (23°C), hypoosmotic (22‰ salinity), ammonium (0.5 mg/L NH4 +-N), and nitrite (0.25 mg/L NO2 --N) stress exposure for 30 days, as well as starvation and crowding (6 kg/m3 density) stress exposure for 60 days. Results demonstrated that all stress led to reduced growth performance and digestive capacity of sea cucumber, along with varying degrees of oxidative stress and immune responses. Various stresses significantly altered the diversity, community structure (except for crowding stress), and composition of intestinal microbiota. The ratios of Bacteroidota: Proteobacteria (B: P) and Firmicutes: Proteobacteria (F: P) declined markedly compared to the control. Potentially pathogenic bacteria of Shewanellaceae, Vibrionaceae, and Moraxellaceae significantly increased under crowding, ammonium, and nitrite stress, respectively, whereas beneficial microbes of Achromobacter and Rhodobacteraceae were, respectively, enriched under hypoosmotic and starvation stresses. The complexity and stability of microbial ecological networks were further altered by these stresses. KEGG predictions revealed the reduced functional pathways of intestinal microbiota involved in host immunity under different stresses. Correlation analysis further confirmed a strong link between microbiota response and host immunity under different stresses. The increased abundance of Verrucomicrobia species could also be identified as the sensitive indicator for diagnosing whether the host was under stressful pressure by random forest analysis.

Nutrition of Escherichia coli within the intestinal microbiome

In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.

Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and Eimeria tenella challenge

Coccidiosis, caused by Eimeria parasites, significantly impacts poultry farm economics and animal welfare. Beyond its direct impact on health, Eimeria infection disrupts enteric microbial populations leading to dysbiosis and increases vulnerability to secondary diseases such as necrotic enteritis, caused by Clostridium perfringens. The impact of Eimeria infection or anticoccidial vaccination on host gastrointestinal phenotypes and enteric microbiota remains understudied. In this study, the metabolomic profiles and microbiota composition of chicken caecal tissue and contents were evaluated concurrently during a controlled experimental vaccination and challenge trial. Cobb500 broilers were vaccinated with a Saccharomyces cerevisiae-vectored anticoccidial vaccine and challenged with 15,000 Eimeria tenella oocysts. Assessment of caecal pathology and quantification of parasite load revealed correlations with alterations to caecal microbiota and caecal metabolome linked to infection and vaccination status. Infection heightened microbiota richness with increases in potentially pathogenic species, while vaccination elevated beneficial Bifidobacterium. Using a multi-omics factor analysis, data on caecal microbiota and metabolome were integrated and distinct profiles for healthy, infected, and recovering chickens were identified. Healthy and recovering chickens exhibited higher vitamin B metabolism linked to short-chain fatty acid-producing bacteria, whereas essential amino acid and cell membrane lipid metabolisms were prominent in infected and vaccinated chickens. Notably, vaccinated chickens showed distinct metabolites related to the enrichment of sphingolipids, important components of nerve cells and cell membranes. Our integrated multi-omics model revealed latent biomarkers indicative of vaccination and infection status, offering potential tools for diagnosing infection, monitoring vaccination efficacy, and guiding the development of novel treatments or controls.IMPORTANCEAdvances in anticoccidial vaccines have garnered significant attention in poultry health management. However, the intricacies of vaccine-induced alterations in the chicken gut microbiome and its subsequent impact on host metabolism remain inadequately explored. This study delves into the metabolic and microbiotic shifts in chickens post-vaccination, employing a multi-omics integration analysis. Our findings highlight a notable synergy between the microbiome composition and host-microbe interacted metabolic pathways in vaccinated chickens, differentiating them from infected or non-vaccinated cohorts. These insights pave the way for more targeted and efficient approaches in poultry disease control, enhancing both the efficacy of vaccines and the overall health of poultry populations.

Updated roles of the gut microbiota in exploring shrimp etiology, polymicrobial pathogens, and disease incidence

Litopenaeus vannamei is the most extensively cultured shrimp species globally, recognized for its scale, production, and economic value. However, its aquaculture is plagued by frequent disease outbreaks, resulting in rapid and massive mortality. etiological research often lags behind the emergence of new diseases, leaving the causal agents of some shrimp diseases unidentified and leading to nomenclature based on symptomatic presentations, especially in cases involving co- and polymicrobial pathogens. Comprehensive data on shrimp disease statuses remain limited. In this review, we summarize current knowledge on shrimp diseases and their effects on the gut microbiome. Furthermore, we also propose a workflow integrating primary colonizers, "driver" taxa in gut networks from healthy to diseased states, disease-discriminatory taxa, and virulence genes to identify potential polymicrobial pathogens. We examine both abiotic and biotic factors (e.g., external and internal sources and specific-disease effects) that influence shrimp gut microbiota, with an emphasis on the "holobiome" concept and common features of gut microbiota response to diverse diseases. After excluding the effects of confounding factors, we provide a diagnosis model for quantitatively predicting shrimp disease incidence using disease common-discriminatory taxa, irrespective of the causal agents. Due to the conservation of functional genes used in designing specific primers, we propose a practical strategy applying qPCR-assayed abundances of disease common-discriminatory functional genes. This review updates the roles of the gut microbiota in exploring shrimp etiology, polymicrobial pathogens, and disease incidence, offering a refined perspective for advancing shrimp aquaculture health management.

The impact of high-salt diet on asthma in humans and mice: Effect on specific T-cell signatures and microbiome

BACKGROUND

The rise in asthma has been linked to different environmental and lifestyle factors including dietary habits. Whether dietary salt contributes to asthma incidence, remains controversial. We aimed to investigate the impact of higher salt intake on asthma incidence in humans and to evaluate underlying mechanisms using mouse models.

METHODS

Epidemiological research was conducted using the UK Biobank Resource. Data were obtained from 42,976 participants with a history of allergies. 24-h sodium excretion was estimated from spot urine, and its association with asthma incidence was assessed by Cox regression, adjusting for relevant covariates. For mechanistic studies, a mouse model of mite-induced allergic airway inflammation (AAI) fed with high-salt diet (HSD) or normal-salt chow was used to characterize disease development. The microbiome of lung and feces (as proxy for gut) was analyzed via 16S rRNA gene based metabarcoding approach.

RESULTS

In humans, urinary sodium excretion was directly associated with asthma incidence among females but not among males. HSD-fed female mice displayed an aggravated AAI characterized by increased levels of total IgE, a TH2-TH17-biased inflammatory cell infiltration accompanied by upregulation of osmosensitive stress genes. HSD induced distinct changes in serum short chain fatty acids and in both gut and lung microbiome, with a lower Bacteroidetes to Firmicutes ratio and decreased Lactobacillus relative abundance in the gut, and enriched members of Gammaproteobacteria in the lung.

CONCLUSIONS

High dietary salt consumption correlates with asthma incidence in female adults with a history of allergies. Female mice revealed HSD-induced T-cell lung profiles accompanied by alterations of gut and lung microbiome.

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.

Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease

The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom.

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.

Study Highlights

The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.

Gut toxicity of polystyrene microplastics and polychlorinated biphenyls to Eisenia fetida: Single and co-exposure effects with a focus on links between gut bacteria and bacterial translocation stemming from gut barrier damage

Microplastics' (MPs) ability to sorb and transport polychlorinated biphenyls (PCBs) in soil ecosystems warrants significant attention. Although organisms mainly encounter pollutants through the gut, the combined pollution impact of MPs and PCBs on soil fauna gut toxicity remains incompletely understood. Consequently, this study examined the gut toxicity of polystyrene MPs (PS-MPs) and PCB126 on Eisenia fetida, emphasizing the links between gut bacteria and bacterial translocation instigated by gut barrier impairment. Our findings underscored that E. fetida could ingest PS-MPs, which mitigated the PCB126 accumulation in E. fetida by 9.43 %. Exposure to PCB126 inhibited the expression of gut tight junction (TJ) protein genes. Although the presence of PS-MPs attenuated this suppression, it didn't alleviate gut barrier damage and bacterial translocation in the co-exposure group. This group demonstrated a significantly increased level of gut bacterial load (BLT, ANOVA, p = 0.005 vs control group) and lipopolysaccharide-binding protein (LBP, ANOVA, all p < 0.001 vs control, PCB, and PS groups), both of which displayed significant positive correlations with antibacterial defense. Furthermore, exposure to PS-MPs and PCB126, particularly within the co-exposure group, results in a marked decline in the dispersal ability of gut bacteria. This leads to dysbiosis (Adonis, R2 = 0.294, p = 0.001), with remarkable signature taxa such as Janthinobacterium, Microbacterium and Pseudomonas, being implicated in gut barrier dysfunction. This research illuminates the mechanism of gut toxicity induced by PS-MPs and PCB126 combined pollution in earthworms, providing novel insights for the ecological risk assessment of soil.

From Mother to Infant, from Placenta to Gut: Understanding Varied Microbiome Profiles in Neonates

The field of human microbiome and gut microbial diversity research has witnessed a profound transformation, driven by advances in omics technologies. These advancements have unveiled essential connections between microbiome alterations and severe conditions, prompting the development of new frameworks through epidemiological studies. Traditionally, it was believed that each individual harbored unique microbial communities acquired early in life, evolving over the course of their lifetime, with little acknowledgment of any prenatal microbial development, but recent research challenges this belief. The neonatal microbiome's onset, influenced by factors like delivery mode and maternal health, remains a subject of intense debate, hinting at potential intrauterine microbial processes. In-depth research reveals associations between microbiome profiles and specific health outcomes, ranging from obesity to neurodevelopmental disorders. Understanding these diverse microbiome profiles is essential for unraveling the intricate relationships between the microbiome and health outcomes.

Systemic inflammatory and gut microbiota responses to fracture in young and middle-aged mice

Age is a patient-specific factor that can significantly delay fracture healing and exacerbate systemic sequelae during convalescence. The basis for this difference in healing rates is not well-understood, but heightened inflammation has been suggested to be a significant contributor. In this study, we investigated the systemic cytokine and intestinal microbiome response to closed femur fracture in 3-month-old (young adult) and 15-month-old (middle-aged) female wild-type mice. Middle-aged mice had a serum cytokine profile that was distinct from young mice at days 10, 14, and 18 post-fracture. This was characterized by increased concentrations of IL-17a, IL-10, IL-6, MCP-1, EPO, and TNFα. We also observed changes in the community structure of the gut microbiota in both young and middle-aged mice that was evident as early as day 3 post-fracture. This included an Enterobacteriaceae bloom at day 3 post-fracture in middle-aged mice and an increase in the relative abundance of the Muribaculum genus. Moreover, we observed an increase in the relative abundance of the health-promoting Bifidobacterium genus in young mice after fracture that did not occur in middle-aged mice. There were significant correlations between serum cytokines and specific genera, including a negative correlation between Bifidobacterium and the highly induced cytokine IL-17a. Our study demonstrates that aging exacerbates the inflammatory response to fracture leading to high levels of pro-inflammatory cytokines and disruption of the intestinal microbiota.

Recent Advances in Cell-Based In Vitro Models to Recreate Human Intestinal Inflammation

Inflammatory bowel disease causes a major burden to patients and healthcare systems, raising the need to develop effective therapies. Technological advances in cell culture, allied with ethical issues, have propelled in vitro models as essential tools to study disease aetiology, its progression, and possible therapies. Several cell-based in vitro models of intestinal inflammation have been used, varying in their complexity and methodology to induce inflammation. Immortalized cell lines are extensively used due to their long-term survival, in contrast to primary cultures that are short-lived but patient-specific. Recently, organoids and organ-chips have demonstrated great potential by being physiologically more relevant. This review aims to shed light on the intricate nature of intestinal inflammation and cover recent works that report cell-based in vitro models of human intestinal inflammation, encompassing diverse approaches and outcomes.

Physical Activity as an Adjunct Treatment for People Living with HIV?

This review evaluates physical activity as a candidate for an adjunct treatment, in conjunction with antiretroviral therapy (ART), for people living with HIV (PLWH). Evidence is summarized that chronic, non-resolving inflammation (a principal feature of immune system dysfunction) and a dysfunctional state of the gut environment are key factors in HIV infection that persist despite treatment with ART. In addition, evidence is summarized that regular physical activity may restore normal function of both the immune system and the gut environment and may thereby ameliorate symptoms and non-resolving inflammation-associated comorbidities that burden PLWH. Physicians who care for PLWH could thus consider incorporating physical activity into treatment plans to complement ART. It is also discussed that different types of physical activity can have different effects on the gut environment and immune function, and that future research should establish more specific criteria for the design of exercise regimens tailored to PLWH.

From adenoma to CRC stages: the oral-gut microbiome axis as a source of potential microbial and metabolic biomarkers of malignancy

BACKGROUND

Approximately 95% of Colorectal cancers (CRC) consist of adenocarcinomas originating from colonic Adenomatous polyps (AP). Increasing importance in CRC occurrence and progression has been attributed to the gut microbiota; however, a huge proportion of microorganisms inhabit the human digestive system. So, to comprehensively study the microbial spatial variations and their role in CRC progression, from AP to the different CRC phases, a holistic vision is imperative, including the simultaneous evaluation of multiple niches from the gastrointestinal system. Through an integrated approach, we identified potential microbial and metabolic biomarkers, able to discriminate human CRC from AP and/or also the different Tumor node metastasis (TNM) staging. In addition, as the microbiota contributes to the production of essential metabolic products detectable in fecal samples, we analysed and compared metabolites obtained from CRC and AP patients by using a Nuclear magnetic resonance (NMR) approach.

METHODS

In this observational study, saliva, tissue and stool samples from 61 patients, have been collected, including 46 CRC and 15 AP patients, age and sex-matched, undergoing surgery in 2018 at the Careggi University Hospital (Florence, Italy). First, the microbiota in the three-district between CRC and AP patients has been characterized, as well as in different CRC TNM stages. Subsequently, proton NMR spectroscopy has been used in combination with multivariate and univariate statistical approaches, to define the fecal metabolic profile of a restricted group of CRC and AP patients.

RESULTS

CRC patients display a different profile of tissue and fecal microbiota with respect to AP patients. Significant differences have been observed in CRC tissue microbial clades, with a rise of the Fusobacterium genus. In addition, significant taxa increase at the genus level has been observed in stool samples of CRC patients. Furthermore, Fusobacterium found in intestinal tissue has been positively correlated with fecal Parvimonas, for the first time. Moreover, as predicted by metagenomics pathway analysis, a significant increase of lactate (p=0.037) has been observed in the CRC fecal metabolic profiles, and positively correlated with Bifidobacterium (p=0.036). Finally, minor bacterial differences in CRC patients at stage T2 (TNM classification) have been detected, with a raise of the Spirochaetota phylum in CRC samples, with a slight increase of the Alphaproteobacteria class in fecal samples.

CONCLUSION

Our results suggest the importance of microbiota communities and oncometabolites in CRC development. Further studies on CRC/AP management with a focus on CRC assessment are needed to investigate novel microbial-related diagnostic tools aimed to improve therapeutic interventions.

A Taxonomy-Agnostic Approach to Targeted Microbiome Therapeutics-Leveraging Principles of Systems Biology

The study of human microbiomes has yielded insights into basic science, and applied therapeutics are emerging. However, conflicting definitions of what microbiomes are and how they affect the health of the "host" are less understood. A major impediment towards systematic design, discovery, and implementation of targeted microbiome therapeutics is the continued reliance on taxonomic indicators to define microbiomes in health and disease. Such reliance often confounds analyses, potentially suggesting associations where there are none, and conversely failing to identify significant, causal relationships. This review article discusses recent discoveries pointing towards a molecular understanding of microbiome "dysbiosis" and away from a purely taxonomic approach. We highlight the growing role of systems biological principles in the complex interrelationships between the gut microbiome and host cells, and review current approaches commonly used in targeted microbiome therapeutics, including fecal microbial transplant, bacteriophage therapies, and the use of metabolic toxins to selectively eliminate specific taxa from dysbiotic microbiomes. These approaches, however, remain wholly or partially dependent on the bacterial taxa involved in dysbiosis, and therefore may not capitalize fully on many therapeutic opportunities presented at the bioactive molecular level. New technologies capable of addressing microbiome-associated diseases as molecular problems, if solved, will open possibilities of new classes and categories of targeted microbiome therapeutics aimed, in principle, at all dysbiosis-driven disorders.

Integration of Transcriptomics and Microbiomics Reveals the Responses of Bellamya aeruginosa to Toxic Cyanobacteria

Frequent outbreaks of harmful cyanobacterial blooms and the cyanotoxins they produce not only seriously jeopardize the health of freshwater ecosystems but also directly affect the survival of aquatic organisms. In this study, the dynamic characteristics and response patterns of transcriptomes and gut microbiomes in gastropod Bellamya aeruginosa were investigated to explore the underlying response mechanisms to toxic cyanobacterial exposure. The results showed that toxic cyanobacteria exposure induced overall hepatopancreatic transcriptome changes. A total of 2128 differentially expressed genes were identified at different exposure stages, which were mainly related to antioxidation, immunity, and metabolism of energy substances. In the early phase (the first 7 days of exposure), the immune system may notably be the primary means of resistance to toxin stress, and it performs apoptosis to kill damaged cells. In the later phase (the last 7 days of exposure), oxidative stress and the degradation activities of exogenous substances play a dominant role, and nutrient substance metabolism provides energy to the body throughout the process. Microbiomic analysis showed that toxic cyanobacteria increased the diversity of gut microbiota, enhanced interactions between gut microbiota, and altered microbiota function. In addition, the changes in gut microbiota were correlated with the expression levels of antioxidant-, immune-, metabolic-related differentially expressed genes. These results provide a comprehensive understanding of gastropods and intestinal microbiota response to toxic cyanobacterial stress.

High nutrient induces virulence in the AHPND-causing Vibrio parahaemolyticus, interpretation from the ecological assembly of shrimp gut microbiota

Shrimp diseases frequently occur during the later farming stages, when the rearing water is eutrophic. This observation provides clue that the virulence of pathogens could be induced by elevated nutrient, whereas the underlying ecological mechanism remains limited. To address this pressing knowledge, we explored how gut microbiota responded to the infection of oligotrophic (OVp) or eutrophic (EVp) pre-cultured Vibrio parahaemolyticus, a causing pathogen of shrimp acute hepatopancreatic necrosis disease (AHPND). Resulted revealed that OVp and EVp infections caused dysbiosis in the gut microbiota and compromised shrimp immunity, while the later infection led to earlier and higher mortality. Significant associations were detected between the gut microbiota and each of the measured immune activities. Neutral community model showed that the assembly of gut microbiota was more strongly governed by deterministic processes in EVp infection, followed by EVp infected and control shrimp. Additionally, there were significantly lower temporal turnover rate and average variation degree in the gut microbiota in EVp infected shrimp compared with control individuals. Notably, we identified 22 infection-discriminatory taxa after ruling out the ontogenic effect. Using profiles of the 22 indicators as independent variables, the diagnosis model accurately distinguished (an overall 85.9% accuracy) the infected status (control, OVp or EVp infected shrimp), with 81.3% accuracy at the initial infection stage. The convergent and deterministic gut microbiota in EVp infected shrimp could partially explain why it is challenge to cure APHND from an ecological viewpoint. In addition, we provided a sensitive approach for diagnosing the onset of infection, when disease symptom is unobservable.

Crohn's disease recurrence updates: first surgery vs. surgical relapse patients display different profiles of ileal microbiota and systemic microbial-associated inflammatory factors

BACKGROUND AND AIMS

Crohn's disease (CD) pathogenesis is still unclear. Remodeling in mucosal microbiota and systemic immunoregulation may represent an important component in tissue injury. Here, we aim to characterize the ileal microbiota in both pathological and healthy settings and to evaluate the correlated systemic microbial-associated inflammatory markers comparing first-time surgery and relapse clinical conditions.

METHODS

We enrolled 28 CD patients at surgery; we collected inflamed and non-inflamed mucosa tissues and blood samples from each patient. Bacterial wall adherence was observed histologically, while its composition was assessed through amplicon sequencing of the 16S rRNA gene. In addition, we evaluated the systemic microRNA (miRNA) using quantitative real-time PCR amplification and free fatty acids (FFAs) using gas chromatography-mass spectroscopy.

RESULTS

The total number of mucosal adherent microbiota was enriched in healthy compared to inflamed mucosa. In contrast, the phylum Tenericutes, the family Ruminococcaceae, and the genera Mesoplasma and Mycoplasma were significantly enriched in the pathological setting. Significant microbiota differences were observed between the relapse and first surgery patients regarding the families Bacillaceae 2 and Brucellaceae and the genera Escherichia/Shigella, Finegoldia, Antrobacter, Gemmatimonas, Moraxella, Anoxibacillus, and Proteus. At the systemic level, we observed a significant downregulation of circulating miR-155 and miR-223, as well as 2-methyl butyric, isobutyric, and hexanoic (caproic) acids in recurrence compared to the first surgery patients. In addition, the level of hexanoic acid seems to act as a predictor of recurrence risk in CD patients (OR 18; 95% confidence interval 1.24-261.81; p = 0.006).

CONCLUSIONS

We describe a dissimilarity of ileal microbiota composition comparing CD and healthy settings, as well as systemic microbial-associated inflammatory factors between first surgery and surgical relapse. We suggest that patterns of microbiota, associated with healthy ileal tissue, could be involved in triggering CD recurrence. Our findings may provide insight into the dynamics of the gut microbiota-immunity axis in CD surgical recurrence, paving the way for new diagnostics and therapeutics aimed not only at reducing inflammation but also at maintaining a general state of eubiosis in healthy tissue.

Gut Epithelial-derived CXCL9 Maintains Gut Homeostasis Through Preventing Overgrown E. coli

BACKGROUND AND AIMS

Increased E. coli in the colon are related to the occurrence and development of multiple diseases. Chemokines are shown to possess potential antimicrobial activity, including against Gram-positive and -negative bacterial pathogens. We here investigated function[s] of chemokine CXCL9 expressed in the gut epithelial cells, and mechanism[s] of CXCL9 by which to kill E. coli.

METHODS

We generated CXCL9fl/flpvillin-creT mice [pvillin-cre positive mice] and their control CXCL9fl/flpvillin-crewmice [pvillin-cre negative mice], and then employed a dextran sulphate sodium [DSS]-mediated colitis model to determine the sensitivity of CXCL9fl/flpvillin-creT mice. We analysed the composition of the gut microbiota by using 16S ribosomal RNA [V3-V4 variable region] sequencing and shotgun metagenomic analyses. We generated E. coli ΔFtsX [FtsX-depleted E. coli] and E. coli ΔaceE [aceE-depleted E. coli] by using a bacterium red recombining system to investigate the mechanism[s] of CXCL9 by which to kill E. coli.

RESULTS

CXCL9 fl/flpvillin-creTmice were more sensitive to chemically induced colitis than their control littermates, CXCL9fl/flpvillin-crewmice. After DSS treatment, there were markedly increased gut E. coli [Escherichia-Shigella] in the colonic contents of CXCL9fl/flpvillin-creT mice as compared with control CXCL9fl/flpvillin-crew mice. The increased E. coli could promote colitis through NLRC4 and caspase 1/11-mediated IL-18, which was derived from gut epithelial cells. We finally demonstrated that CXCL9 expressed in gut epithelial cells could kill the overgrown E. coli. E. coli expressed Ftsx and PDHc subunits aceE. E.coliΔaceE but not E. coliΔFtsX were resistant to CXCL9-mediated killing.

CONCLUSIONS

Gut epithelial cells-derived CXCL9 can kill the expanded E. coli through aceE, to remain gut homeostasis.

Shrimp AHPND Causing Vibrio anguillarum Infection: Quantitative Diagnosis and Identifying Antagonistic Bacteria

Acute hepatopancreatic necrosis disease (AHPND) is one of the most common and serious diseases in shrimp aquaculture. Relevant works have focused on the gut microbiota-disease relationship when serious AHPND occurs. In contrast, little is known about how the gut microbiota responds to pathogen infection over AHPND progression, whereas this knowledge is fundamental to uncover the etiology of AHPND. Here, we explored the temporal succession of shrimp gut microbiota during Vibrio anguillarum (a causal pathogen of AHPND) challenge. The successful infection of V. anguillarum was confirmed by linearly increased abundance of the pathogen in the shrimp gut over AHPND progression. V. anguillarum infection caused an irreversible disruption in the shrimp gut microbiota, of which infection and hours post infection (hpi) respectively constrained 6.2% and 10.2% of variation in the data. Furthermore, the predicted functional pathways involved in immunity and metabolism significantly decreased, while those facilitating infectious diseases significantly enriched in the infected shrimp. Intriguingly, after ruling out the effect of background changes in gut microbiota, we identified 20 infection-discriminatory taxa that could be served as independent variables for accurately (89.4%) diagnosing V. anguillarum infection, even at the early infection stage, i.e., 24 hpi. Using a consensus network, we identified several Vibrio and Pseudoalteromonas taxa that directly antagonized V. anguillarum, following the Darwin's niche theory. This is one of the few attempts to identify gut bioindicators for diagnosing pathogen infection. In addition, the antagonistic commensals of V. anguillarum might be the candidate probiotics for preventing AHPND.

Changes to human faecal microbiota after international travel

BACKGROUND

The aim was to investigate whether travelling to less-resourced destinations influences the composition of faecal microbiota in generally healthy adults.

METHOD

In this prospective observational study, 47 adults (median age, 24 years; 73% females) travelled from Sweden to distant destinations for 1-12 weeks. Five faecal samples, two before and three after travel, were analysed by 16S amplicon massive parallel sequencing. Subjects had taken no antibiotics within three months of each sampling.

RESULTS

The overall composition of faecal microbiota was not affected by travel. However, when looking at the relative abundance of individual bacterial taxa, Enterobacteriaceae demonstrated a 10-fold increase immediately after the trip as compared to the samples taken before travelling. Conversely, the relative abundance of Christensenellaceae had decreased equally much. Both these changes were reversible within nine weeks.

CONCLUSIONS

International travel, even to less-resourced countries, did not appear to alter the overall diversity of human faecal microbiota as studied here after travelling. However, Enterobacteriaceae bacteria, often associated with infection, inflammation, and antibiotic resistance, showed dramatically elevated levels, and Christensenellaceae, frequently associated with healthy conditions, demonstrated remarkably declined levels in relative abundance as detected immediately after travel. Both these changes returned to original pre-travel levels within nine weeks.

Context-dependent effects of glucocorticoids on the lizard gut microbiome

The vertebrate gut microbiota (bacterial, archaeal and fungal communities of the gastrointestinal tract) can have profound effects on the physiological processes of their hosts. Although relatively stable, changes in microbiome structure and composition occur due to changes in the environment, including exposure to stressors and associated increases in glucocorticoid hormones. Although a growing number of studies have linked stressor exposure to microbiome changes, few studies have experimentally explored the specific influence of glucocorticoids on the microbiome in wild animals, or across ecologically important processes (e.g., reproductive stages). Here we tested the response of the gut microbiota of adult female Sceloporus undulatus across gestation to ecologically relevant elevations of a stress-relevant glucocorticoid hormone (CORT) in order to determine (i) how experimentally elevated CORT influenced microbiome characteristics, and (ii) whether this relationship was dependent on reproductive context (i.e., whether females were gravid or not, and, in those that were gravid, gestational stage). We show that the effects of CORT on gut microbiota are complex and depend on both gestational state and stage. CORT treatment altered microbial community membership and resulted in an increase in microbiome diversity in late-gestation females, and microbial community membership varied according to treatment. In nongravid females, CORT treatment decreased interindividual variation in microbial communities, but this effect was not observed in late-gestation females. Our results highlight the need for a more holistic understanding of the downstream physiological effects of glucocorticoids, as well as the importance of context (here, gestational state and stage) in interpreting stress effects in ecology.

Diving into Inflammation: A Pilot Study Exploring the Dynamics of the Immune-Microbiota Axis in Ileal Tissue Layers of Patients with Crohn's Disease

BACKGROUND AND AIMS

The pathogenesis of Crohn's disease [CD] is still unclear. Disorders in the mucosal immunoregulation and its crosstalk with the microbiota may represent an important component in tissue injury. We aimed to characterize the molecular immune response distribution within the ileal layers and to evaluate the correlated microbiota in pathological/healthy settings comparing first surgery/relapse clinical conditions.

METHODS

We enrolled 12 CD patients. A comprehensive analysis of an ileal mucosa, submucosa and serosa broad-spectrum cytokine panel was performed through a multiplex approach. In addition, ileal microbiota composition was assessed through next generation sequencing.

RESULTS

We observed a distinct profile [of IL1-α, IL-1β, IL-4, IL-8, ICAM-1, E-Selectin, P-Selectin, IP-10, IL 6 and IL 18] across the CD vs healthy ileal layers; and a different distribution of IFN- γ, P-Selectin, IL-27 and IL-21 in first surgery vs relapse patients. In addition, the phylum Tenericutes, the family Ruminococcaceae, and the genera Mesoplasma and Mycoplasma were significantly enriched in the pathological setting. Significant microbiota differences were observed between relapse and first surgery patients regarding the class Bacteroidia, and the genera Prevotella, Flavobacterium, Tepidimonas and Escherichia/Shigella. Finally, the abundance of the genus Mycoplasma was positively correlated with IL-18.

CONCLUSIONS

We describe a dissimilarity of cytokine distribution and microbiota composition within CD and adjacent healthy ileal tissue layers and between first operation and surgical relapse. Our results give potential insight into the dynamics of the gut microbiota-immune axis in CD patients, leading to detection of new biomarkers.

Revisiting the steps of Salmonella gut infection with a focus on antagonistic interbacterial interactions

A commensal microbial community is established in the mammalian gut during its development, and these organisms protect the host against pathogenic invaders. The hallmark of noninvasive Salmonella gut infection is the induction of inflammation via effector proteins secreted by the type III secretion system, which modulate host responses to create a new niche in which the pathogen can overcome the colonization resistance imposed by the microbiota. Several studies have shown that endogenous microbes are important to control Salmonella infection by competing for resources. However, there is limited information about antimicrobial mechanisms used by commensals and pathogens during these in vivo disputes for niche control. This review aims to revisit the steps that Salmonella needs to overcome during gut colonization-before and after the induction of inflammation-to achieve an effective infection. We focus on a series of reported and hypothetical antagonistic interbacterial interactions in which both contact-independent and contact-dependent mechanisms might define the outcome of the infection.

Feeding Pre-weaned Calves With Waste Milk Containing Antibiotic Residues Is Related to a Higher Incidence of Diarrhea and Alterations in the Fecal Microbiota

The cows receiving antibiotics for intra-mammary infection (IMI) produce milk that cannot be marketed. This is considered waste milk (WM), and a convenient option for farmers is using it as calf food. However, adding to the risk of selecting resistant bacteria, residual antibiotics might interfere with the gut microbiome development and influence gastrointestinal health. We assessed the longitudinal effect of unpasteurized WM containing residual cefalexin on calf intestinal health and fecal microbiota in an 8-week trial. After 3 days of colostrum, six calves received WM and six calves received bulk tank milk (BM) for 2 weeks. For the following 6 weeks, all 12 calves received milk substitute and starter feed. Every week for the first 2 weeks and every 2 weeks for the remaining 6 weeks, we subjected all calves to clinical examination and collected rectal swabs for investigating the fecal microbiota composition. Most WM calves had diarrhea episodes in the first 2 weeks of the trial (5/6 WM and 1/6 BM), and their body weight was significantly lower than that of BM calves. Based on 16S rRNA gene analysis, WM calves had a lower fecal microbiota alpha diversity than that in BM calves, with the lowest p-value at Wk4 (p < 0.02), 2 weeks after exposure to WM. The fecal microbiota beta diversity of the two calf groups was also significantly different at Wk4 (p < 0.05). Numerous significant differences were present in the fecal microbiota taxonomy of WM and BM calves in terms of relative normalized operational taxonomic unit (OTU) levels, affecting five phyla, seven classes, eight orders, 19 families, and 47 genera. At the end of the trial, when 6 weeks had passed since exposure to WM, the phyla Bacteroidetes, Firmicutes, and Saccharibacteria were lower, while Chlamydiae were higher in WM calves. Notably, WM calves showed a decrease in beneficial taxa such as Faecalibacterium, with a concomitant increase in potential pathogens such as Campylobacter, Pseudomonas, and Chlamydophila spp. In conclusion, feeding pre-weaned calves with unpasteurized WM containing antibiotics is related to a higher incidence of neonatal diarrhea and leads to significant changes in the fecal microbiota composition, further discouraging this practice in spite of its short-term economic advantages.

A Standard Scale to Measure Equine Keeper Status and the Effect of Metabolic Tendency on Gut Microbiome Structure

Simple Summary

Horses with different metabolic tendencies are anecdotally referred to as “easy” or “hard” keepers. Easy keepers tend to gain weight easily while hard keepers require extra feed to maintain condition. Both easy and hard keeper horses carry a managerial and financial burden which can be a dissuading factor for horse shoppers. This research uses energy intake/need and body condition to develop a standard Equine Keeper Status Scale (EKSS) for assigning keeper status. The microbiome compositions based on EKSS assignments are then compared to explore microbiome differences based on metabolic tendencies of each group. The EKSS can be used by owners to accurately assess their horses’ metabolic tendencies and make improved feeding decisions to meet their horses’ needs. Understanding microbiome differences between easy, medium and hard keeper horses points to potential microbial roles in these metabolic tendencies.

Abstract

Thriftiness in horses has been associated with more efficient nutrient harvesting in digestion, absorption and/or utilization, but the relative contribution of the gut microbiome to host metabolic tendency is not well understood. Recognizing the unreliability of owner reported assignment of keeper status, this research describes a novel tool for calculating whether a horse is an easy (EK) or hard (HK) keeper and then characterizes microbiome differences in these groups. The Equine Keeper Status Scale (EKSS) was developed and validated based on data gathered from 240 horses. Estimates of dietary energy intakes and requirements to achieve the optimal BCS score of 5 were used in EKSS assignments. Sixty percent of owners’ characterizations disagreed with EKSS identified keeper assignments. Equine fecal 16S rRNA profiles (n = 73) revealed differences in α and β diversities and taxa abundances based on EKSS assignments. EK communities had more Planctomycetes and fewer Euryarcheaota, Spirochaetes and Proteobacteria than HK indicating functional differences in nutrient harvesting between groups. Differences in the gut microbiomes of horses based on keeper assignment point to host/microbial interactions that may underlie some differences in metabolic tendency. The EKSS enables robust, repeatable determination of keeper status which can be used by researchers and horse owners.

Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis, the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural “traditional” populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae, Coprococcus and Butyrivibrio) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba-negative and Entamoeba-positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis, our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions.

Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages

Neonatal calf diarrhea is a common disease leading to a major economic loss for cattle producers worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. Here, we conducted diagnostic multiplex PCR assay and meta-omics analysis (16S rRNA gene-based metataxonomics and untargeted transcriptional profiling) of rectal content of normal and diarrheic beef calves (n = 111). In the diarrheic calf gut, we detected both microbial compositional dysbiosis (i.e., increased abundances of the family Enterobacteriaceae members and their lytic bacteriophages) and functional dysbiosis (i.e., elevated levels of aerobic respiration and virulence potential). The calf diarrheic transcriptome mirrored the gene expression of the bovine host and was enriched in cellular pathways of sulfur metabolism, innate immunity, and gut motility. We then isolated 12 nontoxigenic Enterobacteriaceae strains from the gut of diarrheic calves. Feeding a strain mixture to preweaning mice resulted in a significantly higher level of fecal moisture content, with decreased body weight gain and shortened colon length. The presented findings suggest that gut inflammation followed by a prolonged expansion of nontoxigenic autochthonous Enterobacteriaceae contributes to the onset of diarrhea in preweaning animals.IMPORTANCE Calf diarrhea is the leading cause of death of neonatal calves worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. The major finding of the current study centers around the observation of microbial compositional and functional dysbiosis in rectal samples from diarrheic calves. These results highlight the notion that gut inflammation followed by a prolonged expansion of autochthonous Enterobacteriaceae contributes to the onset of calf diarrhea. Moreover, this condition possibly potentiates the risk of invasion of notorious enteric pathogens, including Salmonella spp., and the emergence of inflammation-resistant (or antibiotic-resistant) microbiota via active horizontal gene transfer mediated by lytic bacteriophages.

Effects of Antibiotic Treatment with Piperacillin/Tazobactam versus Ceftriaxone on the Composition of the Murine Gut Microbiota

Effective antimicrobial stewardship requires a better understanding of the impact of different antibiotics on the gut microflora. Studies with humans are confounded by large interindividual variability and difficulty in identifying control cohorts. However, controlled murine models can provide valuable information. In this study, we examined the impact of a penicillin-like antibiotic (piperacillin-tazobactam [TZP]) or a third-generation cephalosporin (ceftriaxone [CRO]) on the murine gut microbiota by analysis of changes in fecal microbiome composition by 16S rRNA amplicon sequencing and standard microbiology. Resistance to colonization by multidrug-resistant Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 was also tested. Changes in microbiome composition and a significant (P < 0.05) decrease in diversity occurred in all treated mice, but dysbiosis was more marked and prolonged after CRO exposure, with a persistent rise in Proteobacteria Enterobacteriaceae blooms occurred in all antibiotic-treated mice, but for TZP, unlike CRO, these were significant only under direct antibiotic pressure. At the height of dysbiosis after antibiotic termination, the murine gut was highly susceptible to colonization with both multidrug-resistant enterobacterial pathogens. Cohabitation of treated mice with untreated individuals had a notable mitigating effect on dysbiosis of treated guts. The administration of a third-generation cephalosporin caused a more severe imbalance in the murine fecal microflora than that caused by a penicillin/β-lactam inhibitor combination with comparable activity against medically important virulent bacteria. At the height of dysbiosis, both antibiotic treatments equally led to microbial instability associated with loss of resistance to gut colonization by antibiotic-resistant pathogens.

Intestinal dysbacteriosis leads to kidney stone disease

The formation and physicochemical properties of kidney stones (KSs) are closely associated with diet. In view of the differences in ethnicity and dietary composition between Chinese and Western populations, the present study aimed to investigate the association between intestinal dysbacteriosis and KSs in China. The current study examined the differences in intestinal microbes between the KS disease (KSD) and the healthy control (HLT) groups, and statistically significant differences based on 16s rRNA gene amplicons were identified using a Student's t-test or one-way ANOVA. In addition, the calcium oxalate KS (COKS), uric acid KS (UAKS) and carbonate apatite KS(CCKS) groups were compared with a non-parametric statistical test. Determination of bacterial abundance was performed via the analysis of 16s rRNA marker gene sequences using next-generation sequencing. Firmicutes (F) and Bacteroides (B) levels were significantly higher in the KSD group compared with the HLT group (B/F=0.67 vs. 0.08; P<0.001), as were the overall levels of B (6.19-fold higher compared with the HLT group; 22.2 vs. 3.6%; P<0.001). The Prevotella-9 abundance levels in the KSD group were 4.65-fold higher compared with those in the HLT group (8.8 vs. 1.9%; P<0.001). The levels of Blautia and Lachnoclostridium were significantly decreased in the KSD group (13.3 vs. 6.0%; and 5.0 vs. 7.9%; both P<0.05). Moreover, Prevotella-9 levels were higher in non-calciferous KSs (UAKS) compared with calciferous KSs (COKS and CCKS). Therefore, the findings of the present study indicated a key association between specific KS components and intestinal flora, providing a theoretical basis for new treatment methods for KSs. Moreover, differences and interactions between these bacteria could initially predict specific types of urolithiasis.

Harnessing Iron Acquisition Machinery to Target Enterobacteriaceae

Infections caused by Gram-negative bacteria can be challenging to treat due to the outer membrane permeability barrier and the increasing emergence of antibiotic resistance. During infection, Gram-negative pathogens must acquire iron, an essential nutrient, in the host. Many Gram-negative bacteria utilize sophisticated iron acquisition machineries based on siderophores, small molecules that bind iron with high affinity. In this review, we provide an overview of siderophore-mediated iron acquisition in Enterobacteriaceae and show how these systems provide a foundation for the conceptualization and development of approaches to prevent and/or treat bacterial infections. Differences between the siderophore-based iron uptake machineries of pathogenic Enterobacteriaceae and commensal microbes may lead to the development of selective "Trojan-horse" antimicrobials and immunization strategies that will not harm the host microbiota.

Host-microbiota interactions and responses to grass carp reovirus infection in Ctenopharyngodon idellus

Gut microbiota could facilitate host to defense diseases, but fish-microbiota interactions during viral infection and the underlying mechanism are poorly understood. We examined interactions and responses of gut microbiota to grass carp reovirus (GCRV) infection in Ctenopharyngodon idellus, which is the most important aquaculture fish worldwide. We found that GCRV infection group with serious haemorrhagic symptoms (G7s) showed considerably different gut microbiota, especially with an abnormally high abundance of gram-negative anaerobic Cetobacterium somerae. It also showed the lowest (p < 0.05) alpha-diversity but with much higher ecological process of homogenizing dispersal (28.8%), confirming a dysbiosis of the gut microbiota after viral infection. Interestingly, signaling pathways of NOD-like receptors (NLRs), toll-like receptors (TLRs), and lipopolysaccharide (LPS) stimulation genes were significantly (q-value < 0.01) enriched in G7s, which also significantly (p < 0.01) correlated with the core gut microbial genera of Cetobacterium and Acinetobacter. The results suggested that an expansion of C. somerae initiated by GCRV could aggravate host inflammatory reactions through the LPS-related NLRs and TLRs pathways. This study advances our understanding of the interplay between fish immunity and gut microbiota challenged by viruses; it also sheds new insights for ecological defense of fish diseases with the help of gut microbiota.

Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products

Interleukin (IL)-17 signaling to the intestinal epithelium regulates the intestinal microbiome. Given the reported links between intestinal dysbiosis, bacterial translocation, and liver disease, we hypothesize that intestinal IL-17R signaling plays a critical role in mitigating hepatic inflammation. To test this, we study intestinal epithelium-specific IL-17RA-deficient mice in an immune-driven hepatitis model. At the naive state, these mice exhibit microbiome dysbiosis and increased translocation of bacterial products (CpG DNA), which drives liver IL-18 production. Upon disease induction, absence of enteric IL-17RA signaling exacerbates hepatitis and hepatocyte cell death. IL-18 is necessary for disease exacerbation and is associated with increased activated hepatic lymphocytes based on Ifng and Fasl expression. Thus, intestinal IL-17R regulates translocation of TLR9 ligands and constrains susceptibility to hepatitis. These data connect enteric Th17 signaling and the microbiome in hepatitis, with broader implications on the effects of impaired intestinal immunity and subsequent release of microbial products observed in other extra-intestinal pathologies.

Castillo-dela Cruz et al. describe a unique protective role of intestinal IL-17RA in hepatitis. Disruption of intestinal IL-17RA signaling results in microbiome dysbiosis and translocation of bacterial products, specifically unmethylated CpG DNA, to the liver. This promotes IL-18 production and subsequent lymphocyte activation and cell death to exacerbate liver inflammation.

Reg4 and complement factor D prevent the overgrowth of E. coli in the mouse gut

The expansion of Enterobacteriaceae, such as E. coli is a main characteristic of gut inflammation and is related to multiple human diseases. However, how to control these E. coli overgrowth is not well understood. Here, we demonstrate that gut complement factor D (CFD) plays an important role in eliminating E. coli. Increased E. coli, which could stimulate inflammatory macrophages to induce colitis, were found in the gut of CFD deficient mice. We also showed that gut Reg4, which is expressed in gut epithelial cells, stimulated complement-mediated attack complexes to eliminate E. coli. Reg4 deficient mice also had increased E. coli. The dominant E. coli were isolated from colitis tissues of mice and found to be sensitive to both CFD- and Reg4-mediated attack complexes. Thus, gut Reg4- and CFD-mediated membrane attack complexes may maintain gut homeostasis by killing inflammatory E. coli.

Qi et al. show that gut complement factor D (CFD) plays an important role in eliminating Escherichia coli, using gut specific CFD null mice. They find that E. coli isolated from inflamed guts are sensitive to both CFD and Reg4-mediated attack complexes. This study provides insights into how the level of E. Coli is kept low in the gut to prevent its inflammation.

Niche Specific Microbiota-Dependent and Independent Bone Loss around Dental Implants and Teeth

Oral mucosal homeostasis is achieved by complex immunologic mechanisms, orchestrating host immunity to adapt to the physiologic functions of the various specialized niches in the oral cavity. Dental implants introduce a novel mucosal niche to the immune system to deal with. Nevertheless, the immune mechanisms engaged toward implants and whether they have broader effects are not well defined. Using a murine model, we found an accumulation of neutrophils and RANKL-expressing T and B lymphocytes in the implant-surrounding mucosa, accompanied by local bone loss. Surprisingly, the presence of implants had an impact on remote periodontal sites, as elevated inflammation and accelerated bone loss were detected in intact distant teeth. This was due to microbial dysbiosis induced by the implants, since antibiotic treatment prevented bone loss around teeth. However, antibiotic treatment failed to prevent the loss of implant-supporting bone, highlighting the distinct mechanisms mediating bone loss at each site. Further analysis revealed that implants induced chronic lymphocyte activation and increased mRNA expression of IFN-α and accumulation of IFN-α–producing plasmacytoid dendritic cells, which we previously reported as bone-destructive immune responses. Collectively, this study demonstrates that implants have a strong and broad impact on oral mucosal homeostasis, inducing periodontal bone loss in a niche-specific manner that is both microbiota dependent and independent.

Immune and gut bacterial successions of large yellow croaker (Larimichthys crocea) during Pseudomonas plecoglossicida infection

Large yellow croaker (Larimichthys crocea, LYC) aquaculture is being threatened by intensive infectious diseases. Relevant studies have focused on LYC immune responses to infection. By contrast, little is known how and to what extent the gut microbiota responds to infection. Here, we explored the interactions between LYC immune responses and gut bacterial communities during Pseudomonas plecoglossicida infection. P. plecoglossicida successfully colonized into LYC gut microbiota, resulting in an increasing mortality rate. Relative gene expressions of pro-inflammatory cytokines (TNF-α1, TNF-α2 and IL-1β) and anti-inflammatory cytokine (IL-10) were consistently and significantly induced by P. plecoglossicida infection, whereas non-specific immune enzymes activities were only enhanced at the early infection stages. P. plecoglossicida infection caused an irreversible disruption in the gut microbiota, of which infection and hours post infection constrained 16.2% and 5.6% variations, respectively. In addition, top 18 discriminatory taxa that were responsible for the difference between treatments were identified, whose abundances were significantly associated with the immune activities of LYC. Using a structural equation modeling (SEM), we found that gut bacterial communities were primarily governed by the conjointly direct (-0.33) and indirect (0) effects of infection, which subsequently affect host immune responses. Our results suggest that an irreversible dysbiosis in gut microbiota could be the causality of increasing mortality. To our knowledge, this is the first study to provide an integrated overview among pathogen infection, immune response and gut microbiota of LYC.

Campylobacter Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study

Campylobacter jejuni is a leading cause of bacterial diarrhea worldwide and is associated with high rates of mortality and growth stunting in children inhabiting low- to middle-resource countries. To better understand the impact of breastfeeding on Campylobacter infection in infants in sub-Saharan Africa and South Asia, we examined fecal microbial compositions, bacterial isolates, and their carbohydrate metabolic pathways in Campylobacter-positive infants <1 year of age from the Global Enterics Multicenter Study. Exclusively breastfed infants with diarrhea exhibited high Campylobacter abundances, and this negatively correlated with bacterial carbohydrate metabolism. Although C. jejuni and Campylobacter coli are prevalent among these infants, the second most abundant Campylobacter species was a new species, which we named "Candidatus Campylobacter infans." Asymptomatic Campylobacter carriers also possess significantly different proportions of specific gut microbes compared to diarrheal cases. These findings provide insight into Campylobacter infections in infants in sub-Saharan Africa and South Asia and help inform strategies aimed at eliminating campylobacteriosis in these areas.IMPORTANCECampylobacter is the primary cause of bacterial diarrhea in the United States and can lead to the development of the postinfectious autoimmune neuropathy known as Guillain-Barré syndrome. Also, drug-resistant campylobacters are becoming a serious concern both locally and abroad. In low- and middle-income countries (LMICs), infection with Campylobacter is linked to high rates of morbidity, growth stunting, and mortality in children, and breastfeeding is important for infant nutrition, development, and protection against infectious diseases. In this study, we examined the relationship between breastfeeding and Campylobacter infection and demonstrate the increased selection for C. jejuni and C. coli strains unable to metabolize fucose. We also identify a new Campylobacter species coinfecting these infants with a high prevalence in five of the seven countries in sub-Saharan Africa and South Asia examined. These findings indicate that more detailed studies are needed in LMICs to understand the Campylobacter infection process in order to devise a strategy for eliminating this pathogenic microbe.

Dysbiosis of lower respiratory tract microbiome are associated with inflammation and microbial function variety

BACKGROUND

Lower respiratory tract (LRT) microbiome has been reported to associate with pulmonary diseases. Unregulated inflammation is an underlying cause of variable lung diseases. The lung microbiome may play an important role in the smoking-induced inflammatory lung diseases. What's more, the function of microbiome may be more important for understanding how microbes interact with host. Our study aims to explore the effects of smoking on the lower respiratory tract microbiome, the association between variation of lower respiratory tract microbiome and inflammation and whether smoking exposure changes the function of lower respiratory tract microbime.

METHODS

Forty male mice were randomly divided into smoking group and non-smoking group, and the smoking group was exposed to cigarette smoke for 2 h per day for 90 days. After experiment, the blood samples were collected to measure the concentration of interleukin-6 (IL-6) and C reactive protein (CRP) by ELISA. Lung tissue samples were used to detect the community and diversity of lower respiratory tract microbiome through 16S rRNA gene quantification and sequencing technology. ANOSIM and STAMP were performed to analyze the differences of the microbial community structure between smoking group and non-smoking group. SPSS 24.0 software was used to analyze the correlations between microbiome and inflammation mediators through scatter plots and Spearman correlation coefficient. Microbial metabolic function was predicted by PICRUSt based on the 16 s rRNA gene quantification and sequencing results. PATRIC database was searched for the potential pathogenic bacteria in lower respiratory tract.

RESULTS

Our results suggested that smoking had markedly effects on the microbiota structure of lower respiratory tract based on Bray-Curtis distance (R2 = 0.084, p = 0.005) and on unweighted uniFrac distance (R2 = 0.131, p = 0.002). Smoking mainly affected the abundance of microbiome which belong to Proteobacteria phyla and Firmicutes phyla. Moreover, our results also found that smoking increased the abundance of Acinetobacter, Bacillus and Staphylococcus, which were defined as pathogenic bacteria. Inflammatory mediators were observed to associate with certain microbiome at every level. Most of microbiome which were associated with inflammation belonged to Proteobacteria phyla or Firmicutes phyla. Moreover, we found that the decreased microbiome in smoking group, including Oceanospirillales, Desulfuromonadales, Nesterenkonia, and Lactobacillaceae, all were negatively correlated with IL-6 or CRP. Based on the level of inflammation, the abundance of microbiome differs. At genus level, Lactobacillus, Pelagibacterium, Geobacter and Zoogloea were significantly higher in smoking group with lower IL-6 concentration. The abundance of microbiome was not observed any statistical difference in subgroups with different weight. Three dominant genus, defined as pathogen, were found higher in the smoking group. The microbial functional prediction analysis revealed that ABC-type transport systems, transcription factors, amino acide transport and metabolism, arginine and proline metabolism et al. were distinctively decreased in smoking group, while the proportions of replication, recombination and repair, ribosome, DNA repair and recombination proteins were increased in smoking group (q < 0.05).

CONCLUSIONS

Members of Proteobacteria phyla and Firmicutes phyla played an important role in the microbial community composition and keeping a relatively balanced homeostasis. Microbiome dysbiosis might break the balance of immune system to drive lung inflammation. There might exist potential probiotics in lower respiratory tract, such as Lactobacillaceae. The altered function of Lower respiratory tract microbiome under smoking exposure may affect the physiological homeostasis of host.

Induction of Inflammatory Macrophages in the Gut and Extra-Gut Tissues by Colitis-Mediated Escherichia coli

Inflammatory macrophages play a critical role in gut and extra-gut inflammatory disorders, which may be promoted through the dysbiosis of gut microbiota. However, it is poorly understood how gut microbiota affect inflammatory macrophages. Here, we found that increased Escherichia coli (E. coli) in inflamed colon may induce inflammatory macrophages in gut and extra-gut tissues. These E. coli are different from other commensal and pathogenic E. coli in genomic components and also in ability to induce inflammatory responses. Dominant E. coli from colitic tissues induce gut inflammatory macrophages through a regulating network consisted of IL-18, IFN-γ, IL-12, and IL-22 in gut tissues. These E. coli also directly activate macrophages. Cytosolic inflammasome components PCKδ, NLRC4, caspase8, and caspase1/11 are involved in E. coli-mediated activation in both gut epithelial cells and macrophages. These disclose a novel mechanism for how dysbiosis of gut microbiota in colitis cause inflammatory macrophages related to multiple diseases.

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Increased commensal E. coli in colitis induce inflammatory macrophages

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Colitic E. coli are different from other commensal and pathogenic E. coli

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Gut inflammatory macrophages by E. coli need IL-18, IFN-γ, IL-12, and IL-22

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PCKδ, NLRC4, caspase8, and caspase1/11 are required for E. coli-mediated activation

Gut Vibes in Parkinson's Disease: The Microbiota-Gut-Brain Axis

Background

The complexity of the pathogenic mechanisms underlying neurodegenerative disorders such as Parkinson's disease (PD) is attributable to multifactorial changes occurring at a molecular level, influenced by genetics and environmental interactions. However, what causes the main hallmarks of PD is not well understood. Recent data increasingly suggest that imbalances in the gut microbiome composition might trigger and/or exacerbate the progression of PD.

Objective

The present review aims to (1) report emerging literature showing changes in microbiota composition of PD patients compared to healthy individuals and (2) discuss how these changes may initiate and/or perpetuate PD pathology.

Methods

We analyzed 13 studies published from 2015 and included in this review. Altered microbial taxa were compiled in a detailed table summarizing bacterial changes in fecal/mucosal samples. The methodology was systematically reviewed across the articles and was also included in a table to facilitate comparisons between studies.

Results

Multiple studies found a reduction in short-chain fatty-acid-producing bacteria that can rescue neuronal damage through epigenetic mechanisms. Overall, the studies showed that changes in the gut microbiota composition might influence colonic inflammation, gut permeability, and α-synuclein aggregation, contributing to the neurogenerative process.

Conclusion

Further studies with larger cohorts and high-resolution sequencing methods are required to better define gut microbiota changes in PD. Furthermore, additional longitudinal studies are required to determine the causal link between these changes and PD pathogenesis as well as to study the potential of the intestinal microbiota as a biomarker.

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical "Microscope" Affect the Biological Interpretation?

Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, selecting a bioinformatics pipeline to analyze high-throughput sequencing data from A to Z remains one of the critical considerations in a case-control microbiota study design. Consequently, the aim of this study was to assess whether the same biological conclusions regarding human gut microbiota composition and diversity could be reached using different bioinformatics pipelines. In this work, we considered four pipelines (mothur, QIIME, kraken and CLARK) with different versions and databases, and examined their impact on the outcome of metagenetic analysis of Ion Torrent 16S sequencing data. We re-analyzed a case-control study evaluating the impact of the colonization of the intestinal protozoa Blastocystis sp. on the human gut microbial profile. Although most pipelines reported the same trends in this case-control study, we demonstrated how the use of different pipelines affects the biological conclusions that can be drawn. Targeted metagenomics must therefore rather be considered as a profiling tool to obtain a broad sense of the variations of the microbiota, rather than an accurate identification tool.

Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits

All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.

Enterobactin-Specific Antibodies Induced by a Novel Enterobactin Conjugate Vaccine

Enterobactin (Ent)-mediated high-affinity iron acquisition is critical for Gram-negative bacteria to survive in the host. Given the bacteriostatic effect of lipocalin resulting from its potent Ent-binding ability, immune intervention directly targeting Ent is promising for iron-dependent pathogen control. Recently, an Ent conjugate vaccine was reported, but it still has several significant weaknesses. In this study, we sought to develop an innovative Ent conjugate vaccine that can induce a high level of antibodies directed against Ent and to provide solid evidence demonstrating siderophore-binding capacity of Ent-specific antibodies. Using a simple method, we successfully conjugated purified Ent to different carriers, including keyhole limpet hemocyanin (KLH), bovine serum albumin, and CmeC, a vaccine candidate for Campylobacter control. Subcutaneous immunization of rabbits with the KLH-Ent conjugate triggered a strong systemic IgG immune response with an up to 16,384-fold increase in IgG titer directed against whole conjugate and an up to 4,096-fold increase in the level of specific anti-Ent IgG. To evaluate the ability of Ent-specific IgG to bind to the Ent derivatives present in vivo, various Ent derivatives were chemically synthesized and a unique enzyme-linked immunosorbent assay method was developed. The Ent-specific IgG also displayed exceptional reactivity to ferric Ent, a linear trimer of Ent, and different salmochelins. Growth assays further demonstrated that the Ent-specific antibodies significantly inhibited Ent-dependent growth of Campylobacter spp. and Escherichia coli Collectively, this study reports an efficient method to prepare a new type of Ent conjugate vaccines for inducing a high level of Ent-specific antibodies, which can bind to various Ent derivatives and display lipocalin-like bacteriostatic features.IMPORTANCE Ent-mediated high-affinity iron acquisition is a universal and critical contributor for Gram-negative pathogens to survive and infect hosts. Published information has supported an innovative immune intervention strategy that directly targets Ent to starve pathogens by limiting the availability of iron to be utilized. Compared to a recently published Ent conjugate, there are three advantages of the vaccine described in this study: ease of preparation, induction of high titer of anti-Ent IgG, and the ability of Ent-specific antibodies to bind various Ent derivatives, including the salmochelins that help enteric pathogens evade sequestration of siderophores by host lipocalins. In addition, the Ent-specific antibodies were demonstrated to function similarly to lipocalin to interfere with the Ent-dependent growth of Campylobacter and E. coli under iron-restricted conditions. This study has significant potential for broader applications to prevent and control various Gram-negative infections in humans and animals.

The role of Blastocystis hominis in the activation of ulcerative colitis

BACKGROUND/AIMS

Several studies have shown that a change in microbiota plays an important role in the pathogenesis of inflammatory bowel disease (IBD). Furthermore, with the emergence in recent studies of differences according to the subtype of IBD and whether the disease is active or in remission, there has started to be research into the relationship between IBD and several microorganisms. Blastocystis hominis is primary among these organisms. The aim of the present study was to determine the role of B. hominis in the acute flare-up of ulcerative colitis (UC).

MATERIALS AND METHODS

A total of 114 patients with UC were included in the study, with 52 in the active phase. The Mayo scoring system was used for the activity index. Patients determined with a flare-up agent other than B. hominis were excluded from the study. Fecal samples of the patients were examined by the polymerase chain reaction method for the presence of B. hominis.

RESULTS

B. hominis positivity was determined in 37 (34%) patients with UC. Of the patients, 17 (32.6%) were in the acute flare-up phase, and 20 (32.2%) were in remission (p=0.961). In 11 (64.7%) of the B. hominis positive patients, the disease severity was determined as mild-moderate (p<0.001).

CONCLUSION

The results of the present study showed that while there was no difference between the active and remission phases in respect of B. hominis presence, there was milder involvement in those determined with B. hominis.

IL23R-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease

BACKGROUND AND AIMS

This study aimed to characterize the mucosa-associated microbiota in ileal Crohn's disease [CD] patients and in healthy controls in terms of host genotype and inflammation status.

METHODS

The mucosa-associated microbiotas of intestinal pinch biopsies from 15 ileal CD patients with mild and moderate disease and from 58 healthy controls were analysed based on 16S ribosomal sequencing to determine microbial profile differences between [1] IL23R, NOD2 and ATG16L1 genotypes in healthy subjects, [2] ileal CD patients and control subjects, and [3] inflamed and non-inflamed mucosal tissue in CD patients.

RESULTS

The protective variant of the IL23R gene [rs11209026] significantly impacted the microbial composition in the ileum of healthy subjects and was associated with an increased abundance of phylotypes within the family Christensenellaceae as well as increases in diversity and richness. Comparative analysis of healthy and non-inflamed CD microbiome samples indicated a notable decrease in the abundance of Faecalibacterium prausnitzii as well as Shannon diversity and richness. Inflamed and non-inflamed ileal samples of CD subjects had high intra-individual stability and inter-individual variability, but no significant alterations in diversity, richness or taxa were identified. Calprotectin correlated positively with the abundance of Proteobacteria and negatively with diversity in the samples from healthy subjects.

CONCLUSIONS

The observation of low diversity and low abundance of beneficial bacteria in healthy control subjects carrying the IL23R [rs11209026] wild-type GG genotype indicates that the gut microbiome is influenced by host genetics and is altered prior to disease diagnosis. Faecal calprotectin may be a potential non-invasive screening tool for dysbiosis in subjects without disorders of intestinal inflammation.

Biochemical but not compositional recovery of skin mucosal microbiome communities after disruption

Background

The microbiomes of animals are complex communities that strongly affect the health of the hosts. Microbiomes on mucosal surfaces have the highest densities and most extensive biochemical exchanges with the hosts. Although antibiotics are potent tools to manage infections, they can disrupt the normal microbiota, causing numerous side effects.

Materials and methods

Taking a community ecology approach, mucosal microbiome community responses to five disruptive conditions (two broad-spectrum antibiotics, a biocide, elevated temperature, and rinsing) were analyzed. Skin of the fish Gambusia affinis was the mucosal model. Microbiome recovery was measured by culturable counts, community biochemical profiles, genetic fingerprinting, and community 16S gene sequencing (rinsing condition only).

Results

Following all disruptions, the total counts rose and then returned to the pre-treatment (PT) level. This overgrowth was confirmed via direct staining and community metabolic activity measurements. After rinsing, diversity decreased and one taxon dominated (family Aeromonadaceae) temporarily, the findings similar to numerous other studies with antibiotics. While the community did not return to the PT taxonomic composition, the biochemical profile did.

Conclusion

This suggests that the biochemical pathways in a community are important during recovery, and a return to the original composition is not required to restore original function.

Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection

Influenza is a major public health concern, and the high mortality rate is largely attributed to secondary bacterial infections. There are several mechanisms through which the virus increases host susceptibility to bacterial colonization, but the micro-environment in lower respiratory tract (LRT) of host, infected with influenza virus, is unclear. To this end, we analyzed the LRT microbiome, transcriptome of lung and metabolome of bronchoalveolar lavage fluid (BALF) in mice inoculated intra-nasally with H1N1 to simulate human influenza, and we observed significant changes in the composition of microbial community and species diversity in the acute (7 days post inoculation or dpi), convalescent (14 dpi) and the recovery (28 dpi) periods. The dominant bacterial class shifted from Alphaproteobacteria to Gammaproteobacteria and Actinobacteria in the infected mice, with a significant increase in the relative abundance of anaerobes and facultative anaerobes like Streptococcus and Staphylococcus. The dysbiosis in the LRT of infected mice was not normalized even in the recovery phase of the infection. In addition, the infected lung transcriptome showed significant differences in the expression levels of genes associated with bacterial infection and immune responses. Finally, the influenza virus infection also resulted in significant changes in the metabolome of the BALF. These alterations in the microbiome, transcriptome, and metabolome of infected lungs were not only appeared at the acute period, but also observed at the recovery period. Furthermore, the infection of influenza virus induced a long-term effect in LRT micro-environmental homeostasis, which may give a chance for the invasion of potential pathogens.

Pathogens, microbiome and the host: emergence of the ecological Koch's postulates

Even though tremendous progress has been made in the last decades to elucidate the mechanisms of intestinal homeostasis, dysbiosis and disease, we are only at the beginning of understanding the complexity of the gut ecosystem and the underlying interaction networks. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. Recent work in these domains clearly indicates that the 'traditional Koch's postulates', which state that a given pathogen leads to a distinct disease, are not valid for all 'infectious' diseases, but that a more complete and complex interpretation of Koch's postulates is needed in order to understand and explain them. This review summarises the current understanding of what defines a healthy gut ecosystem and highlights recent progress in uncovering the interplay between the host, its microbiota and invading intestinal pathogens. Based on these recent findings, we propose a new interpretation of Koch's postulates that we term 'ecological Koch's postulates'.

Intestinal in vitro and ex vivo Models to Study Host-Microbiome Interactions and Acute Stressors

The gut microbiome is extremely important for maintaining homeostasis with host intestinal epithelial, neuronal, and immune cells and this host-microbe interaction is critical during times of stress or disease. Environmental, nutritional, and cognitive stress are just a few factors known to influence the gut microbiota and are thought to induce microbial dysbiosis. Research on this bidirectional relationship as it pertains to health and disease is extensive and rapidly expanding in both in vivo and in vitro/ex vivo models. However, far less work has been devoted to studying effects of host-microbe interactions on acute stressors and performance, the underlying mechanisms, and the modulatory effects of different stressors on both the host and the microbiome. Additionally, the use of in vitro/ex vivo models to study the gut microbiome and human performance has not been researched extensively nor reviewed. Therefore, this review aims to examine current evidence concerning the current status of in vitro and ex vivo host models, the impact of acute stressors on gut physiology/microbiota as well as potential impacts on human performance and how we can parlay this information for DoD relevance as well as the broader scientific community. Models reviewed include widely utilized intestinal cell models from human and animal models that have been applied in the past for stress or microbiology research as well as ex vivo organ/tissue culture models and new innovative models including organ-on-a-chip and co-culture models.