The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea

Vaccine-enhanced competition permits rational bacterial strain replacement in the gut

Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. We show that combining oral vaccination with engineered or selected niche-competitor strains permits pathogen exclusion and strain replacement in the mouse gut lumen. This approach can be applied either prophylactically to prevent invasion of nontyphoidal Salmonella strains, or therapeutically to displace an established Escherichia coli. Both intact adaptive immunity and metabolic niche competition are necessary for efficient vaccine-enhanced competition. Our findings imply that mucosal antibodies have evolved to work in the context of gut microbial ecology by influencing the outcome of competition. This has broad implications for the elimination of pathogenic and antibiotic-resistant bacterial reservoirs and for rational microbiota engineering.

Administration of a Recombinant Fusion Protein of IFN-γ and CD154 Inhibited the Infection of Chicks with Salmonella enterica

The cytokines IFN-γ and CD154 have been well established, and they play pivotal roles in immune protection against Salmonella in mice, but their effects and specific mechanisms in Salmonella-infected chickens are less understood. In this study, we conducted animal experiments to screen the highly immunoprotective chIFN-γ-chCD154 fusion protein compared with single protein chIFN-γ or chCD154 in white Leghorn chickens. The results showed that compared with separate pretreatments with chIFN-γ and chCD154, the fusion protein, chIFN-γ-chCD154, synergistically increased survival of infected chickens, reduced bacterial load in feces and organs, and attenuated pathological damage to the liver and cecum. Pretreatment with chIFN-γ-chCD154 also increased humoral immune responses, expression of the tight junction proteins zo-1, occludin, and claudin-1, and the relative abundance of Enterococcus_cecorum, Lactobacillus_helveticus, and Lactobacillus_agilis, which protect against intestinal inflammation. Compared with single protein pretreatment, chIFN-γ-chCD154 significantly upregulated STAT1, IRF1, and GBP1 in infected chickens while decreasing mRNA expression of TLR4, MyD88, NF-κB, TNF-α, IL-6, and IL-1β. In summary, damage to the cecal epithelial barrier and the inflammation induced by S. typhimurium infection was alleviated by chIFN-γ-chCD154 pretreatment through a mechanism involving the TLR4/MyD88/NF-κB and IFN-γ/STAT/IRF1/GBP1 pathways.

Gastrointestinal germinal center B cell depletion and reduction in IgA+ plasma cells in HIV-1 infection

Gastrointestinal (GI) B cells and plasma cells (PCs) are critical to mucosal homeostasis and the host response to HIV-1 infection. Here, high-resolution mapping of human B cells and PCs sampled from the colon and ileum during both viremic and suppressed HIV-1 infection identified a reduction in germinal center (GC) B cells and follicular dendritic cells (FDCs) during HIV-1 viremia. Immunoglobulin A-positive (IgA+) PCs are the major cellular output of intestinal GCs and were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling, persisted in antiretroviral therapy (ART)-treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations were associated with changes in the intestinal microbiome composition and systemic inflammation. These findings highlight a key immune defect in the GI mucosa due to HIV-1 viremia.

A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency

Harnessing the microbiome to benefit human health requires an initial step in determining the identity and function of causative microorganisms that affect specific host physiological functions. We show a functional screen of the bacterial microbiota from mice with low intestinal immunoglobulin A (IgA) levels; we identified a Gram-negative bacterium, proposed as Tomasiella immunophila, that induces and degrades IgA in the mouse intestine. Mice harboring T. immunophila are susceptible to infections and show poor mucosal repair. T. immunophila is auxotrophic for the bacterial cell wall amino sugar N-acetylmuramic acid. It delivers immunoglobulin-degrading proteases into outer membrane vesicles that preferentially degrade rodent antibodies with kappa but not lambda light chains. This work indicates a role for symbionts in immunodeficiency, which might be applicable to human disease.

Distribution characteristics of gastric mucosal colonizing microorganisms in different glandular regions of Bactrian camels and their relationship with local mucosal immunity

Bactrian camels inhabiting desert and semi-desert regions of China are valuable animal models for studying adaptation to desert environments and heat stress. In this study, 16S rRNA technology was employed to investigate the distribution characteristics and differences of mucosal microorganisms in the anterior gland area, posterior gland area, third gland area, cardia gland area, gastric fundic gland area and pyloric gland area of 5-peak adult healthy Bactrian camels. We aimed to explore the possible reasons for the observed microbial distribution from the aspects of histological structure and mucosal immunity. Bacteroides and Fibrobacteria accounted for 59.54% and 3.22% in the gland area, respectively, and 52.37% and 1.49% in the wrinkled stomach gland area, respectively. The gland area showed higher abundance of Bacteroides and Fibrobacteria than the wrinkled stomach gland area. Additionally, the anterior gland area, posterior gland area, third gland area, and cardia gland area of Bactrian camels mainly secreted acidic mucus, while the gastric fundic gland area mainly secreted neutral mucus and the pyloric region mainly secreted a mixture of acidic and neutral mucus. The results of immunohistochemistry techniques demonstrated that the number of IgA+ cells in the anterior glandular area, posterior glandular area, third glandular area, and cardia gland area was significantly higher than that in the fundic and pyloric gland area (p < 0.05), and the difference in IgA+ between the fundic and pyloric gland area was not significant (p > 0.05). The study revealed a large number of bacteria that can digest and degrade cellulose on the mucosa of the gastric gland area of Bactrian camels. The distribution of IgA+ cells, the structure of the mucosal tissue in the glandular region, and the composition of the mucus secreted on its surface may have a crucial influence on microbial fixation and differential distribution.

Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay

Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.

Colonization resistance: the role of gut microbiota in preventing Salmonella invasion and infection

The human gastrointestinal tract is colonized by a complex microbial ecosystem, the gut microbiota, which is pivotal in maintaining host health and mediating resistance to diseases. This review delineates colonization resistance (CR), a critical defensive mechanism employed by the gut microbiota to safeguard against pathogenic bacterial invasions, notably by Salmonella. We detail the mechanisms through which the gut microbiota impedes Salmonella colonization, including nutrient competition, production of antimicrobial peptides, synthesis of microbial-derived metabolites, and modulation of the host immune response. Additionally, we examine how dietary interventions can influence these mechanisms, thereby augmenting the protective role of the gut microbiota. The review also discusses the sophisticated strategies utilized by Salmonella to overcome these microbial defenses. A thorough understanding of these complex interactions between microbial symbionts and pathogens is crucial for the development of innovative therapeutic strategies that enhance CR, aiming to prevent or treat microbial infections effectively.

Clinical Analysis of Bacterial Infection Characteristics in Lymphoma Patients with High-dose Chemotherapy Combined with Autologous Hematopoietic Stem Cell Transplantation-A Single-Centered Retrospective Study

BACKGROUND

High-dose chemotherapy combined with autologous hematopoietic stem cell transplantation (HDT/AHSCT) is used to treat lymphoma. Although AHSCT has made considerable strides and become safer, HDT-AHSCT infection continues to be a leading cause of morbidity and mortality associated with transplantation.

OBJECTIVE

To characterise pathogenic bacterial infections in HDT/AHSCT-treated lymphoma patients. The prevalence of pathogenic microorganisms and the timing of foci after transplantation, along with bloodstream infection (BSI) risk factors, can help determine the need for empirical antibiotics after AHSCT.

METHODS

We retrospectively analyzed 133 lymphoma patients treated by HDT/AHSCT from April 2017 to October 2021 at Peking University International Hospital, Beijing, China. We analyzed their clinical characteristics, microbiological distribution characteristics, and BSI risk factors in detail.

RESULTS

In order, intestinal infection (56 cases), BSI (17 cases), pulmonary (12 cases), upper respiratory tract (5 cases), and perianal (4 cases) were the most common locations of infection after HDT/AHSCT. The infection sites yielded 92 putative pathogenic pathogens, with bacteria predominating (61.96%), fungi (28.26%), viruses (5.43%), and mycoplasma (4.35%). Gram-negative bacteria (GNB) strains outnumbered gram-positive bacteria (GPB) strains (73.68%). Two strains of Escherichia coli produced extended-spectrum β-lactamase (ESBL) and one strain of carbapenem-resistant enterobacteriaceae (CRE). Methicillin-resistant Staphylococcus epidermidis (MRSE) had one strain. BSI was caused by Escherichia coli (82.35%), Intestinal mucositis (23.52%), and catheter-associated infections (11.76%). Age, CD34, pretreatment regimen, antibiotic regimen, and past chemotherapeutic agent lung damage were BSI risk variables in univariate analysis. CD34 and past chemotherapeutic drug lung damage were the primary causes of BSI after HDT/AHSCT for lymphoma.

CONCLUSION

High-dose chemotherapy combined with autologous hematopoietic stem cell transplantation (HDT/AHSCT) is used to treat lymphoma. Although AHSCT has made considerable strides and become safer, HDT-AHSCT infection continues to be a leading cause of morbidity and mortality associated with transplantation.

From microbiome composition to functional engineering, one step at a time

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Salmonella delivers H9N2 influenza virus antigens via a prokaryotic and eukaryotic dual-expression vector and elicits bivalent protection against avian influenza and fowl typhoid

The H9N2 avian influenza virus significantly affects the health of poultry and humans. We identified a prokaryotic and eukaryotic dual-expression vector system, pJHL270, that can provide simultaneous MHC class I and II stimulation of the host immune system, and we designed vaccine antigens by selecting the consensus HA1 sequence and M2e antigens from H9N2 virus circulating in South Korea from 2000 to 2021. The genes were cloned into the pJHL270 vector, and the cloned plasmid was delivered by a live-attenuated Salmonella Gallinarum (SG) strain. The immunity and protective efficacy of the SG-based H9N2 vaccine construct, JOL2922, against avian influenza and fowl typhoid (FT) were evaluated. The Ptrc and CMV promoters conferred antigen expression in prokaryotic and eukaryotic cells to induce balanced Th-1/Th-2 immunity. Chickens immunized with JOL2922 yielded high antigen-specific humoral and mucosal immune responses. qRT-PCR revealed that the strain generated polyfunctional IFN-γ and IL-4 secretion in immunized chickens. Furthermore, a FACS analysis showed increased CD3CD4+ and CD3CD8+ T-cell subpopulations following immunization. Peripheral Blood Mononuclear Cells (PBMCs) harvested from the immunized chickens significantly increased MHC class I and II expression, 3.5-fold and 2.5-fold increases, respectively. Serum collected from the immunized groups had an evident hemagglutinin inhibition titer of ≥6 log2. Immunization reduced the lung viral titer by 3.8-fold within 5 days post-infection. The strain also generated SG-specific humoral and cellular immune responses. The immunized birds all survived a virulent SG wild-type challenge. In addition, the bacterial burden was reduced by 2.7-fold and 2.1-fold in spleen and liver tissue, respectively, collected from immunized chickens. Our data indicate that an attenuated SG strain successfully delivered the dual-expression vector system and co-stimulated MHC class I and II antigen presentation pathways via exogenous and endogenous antigen presentation, thereby triggering a balanced Th-1/Th-2-based immune response and conferring effective protection against avian influenza and FT.

Glyphosate decreases survival, increases fecundity, and alters the microbiome of the natural predator Harmonia axyridis (ladybird beetle)

Glyphosate is a widely-used herbicide that shows toxicity to non-target organisms. The predatory natural enemy Harmonia axyridis may ingest glyphosate present in pollen and aphid prey. The present study characterized the responses of adult H. axyridis to environmentally relevant concentrations of glyphosate (5, 10, and 20 mg/L) for one or five days. There were no obvious effects on adult H. axyridis survival rates or fecundity in response to 5 or 10 mg/L glyphosate. However, exposure to 20 mg/L glyphosate significantly reduced the survival rate and increased fecundity. Analysis of the adult H. axyridis microbiota with 16S rRNA sequencing demonstrated changes in the relative and/or total abundance of specific taxa, including Serratia, Enterobacter, Staphylococcus, and Hafnia-Obesumbacterium. These changes in symbiotic bacterial abundance may have led to changes in survival rates or fecundity of this beetle. This is the first report of herbicide-induced stimulation of fecundity in a non-target predatory natural enemy, reflecting potentially unexpected risks of glyphosate exposure in adult H. axyridis. Although glyphosate resistant crops have been widely planted, the results of this study indicate a need to strengthen glyphosate management to prevent over-use, which could cause glyphosate toxicity and threaten environmental and human health.

Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya

Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.

An insight into the functional alterations in the gut microbiome of healthy adults in response to a multi-strain probiotic intake: a single arm open label trial

Background

Probiotic supplements, by definition, provide a benefit to the host, but few studies have investigated the effect of probiotic supplements in healthy adult populations.

Purpose

The present, single arm, open label clinical trial, evaluated compositional and functional changes in the fecal microbiome of healthy adults after supplementation with a 14-strain probiotic.

Methods

We analysed the effect of a 14-strain probiotic blend (Bacillus subtilis NCIMB 30223, Bifidobacterium bifidum NCIMB 30179, B. breve NCIMB 30180, B. infantis NCIMB 30181, B. longum NCIMB 30182, Lactobacillus helveticus NCIMB 30184, L. delbrueckii subsp. bulgaricus NCIMB 30186, Lacticaseibacillus paracasei NCIMB 30185, Lactiplantibacillus plantarum NCIMB 30187, Lacticaseibacillus rhamnosus NCIMB 30188, L. helveticus NCIMB 30224, Lactobacillus salivarius NCIMB 30225, Lactococcus lactis subsp. lactis NCIMB 30222, and Streptococcus thermophilus NCIMB 30189), on the faecal microbiota of healthy young adults (n=41) in a single arm study. The adults consumed 4 capsules daily of the 14 strain blend(8 billion colony forming units/day) for 8 weeks. Compositional and functional changes in faecal microbiota before and after supplementation were assessed using shotgun metagenomic sequencing. Fasting breath analysis, faecal biochemistry and bowel habits were also assessed.

Results

In healthy adult participants, no significant changes to the overall alpha- or beta-diversity was observed after 8 weeks of multi-strain probiotic supplementation. However, in a simplified model that considered only time and individual differences, significant decreases (p < 0.05) in family Odoribacteraceae and Bacteroidaceae abundance and a significant increase (p < 0.05) in genus Megamonas abundance were observed. At a functional level, there were significant changes in functional gene abundance related to several functional pathways, including phenylalanine metabolism, O-antigen nucleotide sugar biosynthesis, bacterial chemotaxis, and flagellar assembly. No significant changes in stool form or frequency, fecal biochemistry, or methane and hydrogen breath tests were observed.

Conclusion

In healthy young adults, overall alpha- and beta-diversity did not change in response to probiotic intake even though modest compositional changes at the family and genus level were observed. However, at functional level, results identified changes in gene abundance for several functional pathways.

License to Clump: Secretory IgA Structure-Function Relationships Across Scales

Secretory antibodies are the only component of our adaptive immune system capable of attacking mucosal pathogens topologically outside of our bodies. All secretory antibody classes are (a) relatively resistant to harsh proteolytic environments and (b) polymeric. Recent elucidation of the structure of secretory IgA (SIgA) has begun to shed light on SIgA functions at the nanoscale. We can now begin to unravel the structure-function relationships of these molecules, for example, by understanding how the bent conformation of SIgA enables robust cross-linking between adjacent growing bacteria. Many mysteries remain, such as the structural basis of protease resistance and the role of noncanonical bacteria-IgA interactions. In this review, we explore the structure-function relationships of IgA from the nano- to the metascale, with a strong focus on how the seemingly banal "license to clump" can have potent effects on bacterial physiology and colonization.

"EvoVax" - A rationally designed inactivated Salmonella Typhimurium vaccine induces strong and long-lasting immune responses in pigs

Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm) poses a considerable threat to public health due to its zoonotic potential. Human infections are mostly foodborne, and pork and pork products are ranked among the top culprits for transmission. In addition, the high percentage of antibiotic resistance, especially in monophasic S.Tm, limits treatment options when needed. Better S.Tm control would therefore be of benefit both for farm animals and for safety of the human food chain. A promising pre-harvest intervention is vaccination. In this study we tested safety and immunogenicity of an oral inactivated S.Tm vaccine, which has been recently shown to generate an "evolutionary trap" and to massively reduce S.Tm colonization and transmission in mice. We show that this vaccine is highly immunogenic and safe in post-weaning pigs and that administration of a single oral dose results in a strong and long-lasting serum IgG response. This has several advantages over existing - mainly live - vaccines against S.Tm, both in improved seroconversion and reduced risk of vaccine-strain persistence and reversion to virulence.

The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence

Salmonella Typhimurium elicits gut inflammation by the costly expression of HilD-controlled virulence factors. This inflammation alleviates colonization resistance (CR) mediated by the microbiota and thereby promotes pathogen blooms. However, the inflamed gut-milieu can also select for hilD mutants, which cannot elicit or maintain inflammation, therefore causing a loss of the pathogen's virulence. This raises the question of which conditions support the maintenance of virulence in S. Typhimurium. Indeed, it remains unclear why the wild-type hilD allele is dominant among natural isolates. Here, we show that microbiota transfer from uninfected or recovered hosts leads to rapid clearance of hilD mutants that feature attenuated virulence, and thereby contributes to the preservation of the virulent S. Typhimurium genotype. Using mouse models featuring a range of microbiota compositions and antibiotic- or inflammation-inflicted microbiota disruptions, we found that irreversible disruption of the microbiota leads to the accumulation of hilD mutants. In contrast, in models with a transient microbiota disruption, selection for hilD mutants was prevented by the regrowing microbiota community dominated by Lachnospirales and Oscillospirales. Strikingly, even after an irreversible microbiota disruption, microbiota transfer from uninfected donors prevented the rise of hilD mutants. Our results establish that robust S. Typhimurium gut colonization hinges on optimizing its manipulation of the host: A transient and tempered microbiota perturbation is favorable for the pathogen to both flourish in the inflamed gut and also minimize loss of virulence. Moreover, besides conferring CR, the microbiota may have the additional consequence of maintaining costly enteropathogen virulence mechanisms.

The role of probiotics in tissue engineering and regenerative medicine

Tissue engineering and regenerative medicine (TERM) as an emerging field is a multidisciplinary science and combines basic sciences such as biomaterials science, biology, genetics and medical sciences to achieve functional TERM-based products to regenerate or replace damaged or diseased tissues or organs. Probiotics are useful microorganisms which have multiple effective functions on human health. They have some immunomodulatory and biocompatibility effects and improve wound healing. In this article, we describe the latest findings on probiotics and their pro-healing properties on various body systems that are useable in regenerative medicine. Therefore, this review presents a new perspective on the therapeutic potential of probiotics for TERM.

Determinants of persistent Salmonella infections

Persistent bacterial infections constitute an enormous challenge for public health. Amongst infections with other bacteria, infections with typhoidal and nontyphoidal Salmonella enterica serovars can result in long-term infections of the human and animal host. Persistent infections that are asymptomatic are difficult to identify and thus can serve as a silent reservoir for transmission. Symptomatic persistent infections are often difficult to treat as they harbor a combination of antibiotic-tolerant and antibiotic-resistant bacteria and boost the spread of genetic antibiotic resistance. In the last couple of years, the field has made some major progress in understanding the role of persisters, their reservoirs as well as their interplay with host factors in persistent Salmonella infections.

Tachinid parasitoid Exorista japonica affects the utilization of diet by changing gut microbial composition in the silkworm, Bombyx mori

Changes in both intake and digestion of feed have been demonstrated in the host following parasitization. However, its regulatory mechanism has not been clarified. In this study, silkworms and Exorista japonica were used as research objects to analyze the effect of parasitism on the midgut immune system of the silkworm. After being parasitized, the expressions of antimicrobial peptide (AMP) genes of silkworms showed a fluctuating trend of first upregulation and then downregulation, while phenoloxidase and lysozyme activities were inhibited. To study the possible impact of the downregulation of AMP genes on intestinal microorganisms, the characteristics of the intestinal microbial population of silkworms on the third day of parasitism were analyzed. The relative abundance of Firmicutes, Proteobacteria, and Bacteroidota decreased, while that of Actinobacteriota increased. The increased abundance of conditionally pathogenic bacteria Serratia and Staphylococcus might lead to a decrease in the amount of silkworm ingestion. Meanwhile, the abundance of Acinetobacter, Bacillus, Pseudomonas, and Enterobacter promotes an increase in the digestion of nutrients. This study indicated that the imbalance of intestinal microbial homeostasis caused by parasitism may affect the absorption and digestion of nutrients by the host. Collectively, our findings provided a new clue for further exploring the mechanism of nutrient transport among the host, parasitoid, and intestinal microorganisms.

Microbial diversity in stingless bee gut is linked to host wing size and influenced by the environment

Stingless bees are important social corbiculate bees, fulfilling critical pollination roles in many ecosystems. However, their gut microbiota, particularly the fungal communities associated with them, remains inadequately characterised. This knowledge gap hinders our understanding of bee gut microbiomes and their impacts on the host fitness. We collected 121 samples from two species, Tetragonula carbonaria and Austroplebeia australis across 1200 km of eastern Australia. We characterised their gut microbiomes and investigated potential correlations between bee gut microbiomes and various geographical and morphological factors. We found their core microbiomes consisted of the abundant bacterial taxa Snodgrassella, Lactobacillus and Acetobacteraceae, and the fungal taxa Didymellaceae, Monocilium mucidum and Aureobasidium pullulans, but variances of their abundances among samples were large. Furthermore, gut bacterial richness of T. carbonaria was positively correlated to host forewing length, an established correlate to body size and fitness indicator in insects relating to flight capacity. This result indicates that larger body size/longer foraging distance of bees could associate with greater microbial diversity in gut. Additionally, both host species identity and management approach significantly influenced gut microbial diversity and composition, and similarity between colonies for both species decreased as the geographic distance between them increased. We also quantified the total bacterial and fungal abundance of the samples using qPCR analyses and found that bacterial abundance was higher in T. carbonaria compared to A. australis, and fungi were either lowly abundant or below the threshold of detection for both species. Overall, our study provides novel understanding of stingless bee gut microbiomes over a large geographic span and reveals that gut fungal communities likely not play an important role in host functions due to their low abundances.

Tango of B cells with T cells in the making of secretory antibodies to gut bacteria

Polymeric IgA and IgM are transported across the epithelial barrier from plasma cells in the lamina propria to exert a function in the gut lumen as secretory antibodies. Many secretory antibodies are reactive with the gut bacteria, and mounting evidence suggests that these antibodies are important for the host to control gut bacterial communities. However, we have incomplete knowledge of how bacteria-reactive secretory antibodies are formed. Antibodies from gut plasma cells often show bacterial cross-species reactivity, putting the degree of specificity behind anti-bacterial antibody responses into question. Such cross-species reactive antibodies frequently recognize non-genome-encoded membrane glycan structures. On the other hand, the T cell epitopes are peptides encoded in the bacterial genomes, thereby allowing a higher degree of predictable specificity on the T cell side of anti-bacterial immune responses. In this Perspective, we argue that the production of bacteria-reactive secretory antibodies is mainly controlled by the antigen specificity of T cells, which provide help to B cells. To be able to harness this system (for instance, for manipulation with vaccines), we need to obtain insight into the bacterial epitopes recognized by T cells in addition to characterizing the reactivity of the antibodies.

Lp-pPG-611.1-LPS as an immune enhancer provides effective protection against Aeromonas veronii infection in Carassius auratus

Aeromonas veronii (A. veronii) is an important zoonotic pathogen that causes substantial economic losses in aquaculture. In this study, we aimed to develop a safe and effective immune enhancer to protect Carassius auratus (C. auratus) from A. veronii infections. With recognized safety, lactic acid bacteria are used as antigen delivery vehicles to present antigens. Lipopolysaccharide (LPS), a protective antigen, induces immune responses in animals. Therefore, we created recombinant Lactobacillus plantarum (L. plantarum) with surface-displayed LPS of A. veronii TH0426 and tested its effects on immune responses in C. auratus. The results showed that recombinant L. plantarum Lp-pPG-611.1-LPS, as an immune enhancer, could improve the innate and adaptive immune responses of C. auratus when it was added to the diet of C. auratus. The challenge test showed that the survival rate of C. auratus fed with L. plantarum Lp-pPG-611.1-LPS was higher than that of the control groups, indicating that the recombinant L. plantarum Lp-pPG-611.1-LPS increased the resistance of C. auratus to A. veronii infection. The present results provide a theoretical basis for the development of recombinant L. plantarum Lp-pPG-611.1-LPS as an immune enhancer in aquaculture.

Competitive ability of <i>Escherichia coli</i> strains in the intestinal microbiota of patients with Crohn's disease and healthy volunteers: physiological, biochemical and genetic characteristics

Introduction. Crohn's disease (CD) is a chronic inflammation of various parts of the gastrointestinal tract with an increased proportion of Escherichia coli. However, the role of E. coli in disease remains unclear. This study aims to evaluate the competitive abilities of E. coli strains from CD patients and healthy volunteers, and to identify the biochemical and genetic determinants underlying these features. Materials and methods. The antagonistic activity was assessed by co-cultivation of 11 clinical E. coli strains inhibiting the growth of the K-12, with Enterobacter cloacae, Klebsiella pneumonia and Salmonella enterica. To elucidate the mechanism of antagonistic activity, the evaluation of biochemical properties and a comparative genomic analysis were used. Results and discussion. Genes of bacteriocin production systems were identified in genomes of 11 strains from CD patients and healthy volunteers active against the E. coli K-12 strain. Three strains from healthy individuals demonstrated activity against several Enterobacteriaceae bacteria. The strains biochemical properties were typical of representatives of E. coli. Strains 1_34_12, active against E. cloacae, and 1_45_11, inhibiting all tested enterobacteria, are phylogenetically related to the laboratory strain K-12. Strain 1_39_1, active against K. pneumonia and S. enterica, is phylogenetically close to the Nissle1917, contains the genes for colibactin biosynthesis and a variant of the fimH gene that increases the adhesive ability of bacteria. Conclusion. The identified E. coli strains are able to displace Enterobacteriaceae bacteria and can be used to study the bacteria-bacteria and host-bacteria interactions, to understand their role in gut homeostasis and intestinal inflammation.

Mouse models for bacterial enteropathogen infections: insights into the role of colonization resistance

Globally, enteropathogenic bacteria are a major cause of morbidity and mortality.1-3 Campylobacter, Salmonella, Shiga-toxin-producing Escherichia coli, and Listeria are among the top five most commonly reported zoonotic pathogens in the European Union.4 However, not all individuals naturally exposed to enteropathogens go on to develop disease. This protection is attributable to colonization resistance (CR) conferred by the gut microbiota, as well as an array of physical, chemical, and immunological barriers that limit infection. Despite their importance for human health, a detailed understanding of gastrointestinal barriers to infection is lacking, and further research is required to investigate the mechanisms that underpin inter-individual differences in resistance to gastrointestinal infection. Here, we discuss the current mouse models available to study infections by non-typhoidal Salmonella strains, Citrobacter rodentium (as a model for enteropathogenic and enterohemorrhagic E. coli), Listeria monocytogenes, and Campylobacter jejuni. Clostridioides difficile is included as another important cause of enteric disease in which resistance is dependent upon CR. We outline which parameters of human infection are recapitulated in these mouse models, including the impact of CR, disease pathology, disease progression, and mucosal immune response. This will showcase common virulence strategies, highlight mechanistic differences, and help researchers from microbiology, infectiology, microbiome research, and mucosal immunology to select the optimal mouse model.

Biochemical indexes and gut microbiota testing as diagnostic methods for Penaeus monodon health and physiological changes during AHPND infection with food safety concerns

Severe shrimp disease outbreaks have a destructive impact on shrimp aquaculture and its associated downstream food processing industries. Thus, it is essential to develop proper methods for shrimp disease control, which emphasizes the importance of food safety. In this study, we performed biochemical tests and gut microbiome analysis using uninfected control and Vp AHPND-infected Penaeus monodon samples. Biochemical tests were performed to assess the phenoloxidase (PO) activity, respiratory Burst (RB) activity, nitrite concentration, superoxide dismutase (SOD) activity, total hemocyte count (THC), and total protein concentrations. Overall, upregulations were detected in these biochemical tests, which showed the activation of the immune response in P. monodon during acute hepatopancreatic necrosis disease (AHPND) infection, especially at 6 hpi and 12 hpi. Besides that, shrimp gut samples were collected and pooled (n = 3), followed by DNA extraction, PCR amplification targeting the V3/V4 16S ribosomal RNA (rRNA) region, next-generation sequencing (NGS), and bioinformatics analysis. Proteobacteria was the most abundant phylum in both samples. The Rhodobacteraceae family and Maritimibacter genus were proposed to be vital forshrimp health maintenance. Vp AHPND bacterial colonization and secondary Vibrio infections were postulated to have occurred based on the higher abundances of Vibrionaceae family and Vibrio genus in the Vp AHPND-infected sample. Firmicutes phylum together with Photobacterium and Aliiroseovarius genera were inferred to be pathogenic or related factors of AHPND infections. In conclusion, physiology (immune response activation) and gut microbiome changes of disease tolerant P. monodon during AHPND infection were identified. Both biochemical tests and 16S rRNA analysis are proposed as a combined strategy for shrimp health diagnosis for ensuring shrimp health maintenance, disease control, and food safety.

Early life administration of Bifidobacterium bifidum BD-1 alleviates long-term colitis by remodeling the gut microbiota and promoting intestinal barrier development

Inflammatory bowel disease (IBD) is a chronic intestinal disease characterized by microbiota disturbance and intestinal mucosal damage. The current study aimed to investigate the preventive effects of Bifidobacterium bifidum BD-1 (BD-1) against long-term IBD and possible mechanism by which it alters the gut microbiota, immune response, and mucosal barrier. Our study found that early treatment of BD-1 + Ceftri (ceftriaxone followed by BD-1) and BD-1 confers a certain protective effect against the occurrence of long-term Dextran sulfate sodium-induced colitis, which manifests as a decrease in inflammation scores and MPO activity levels, as well as a relatively intact intestinal epithelial structure. Moreover, compared to BD-1, Ceftri, and NS, early treatment with BD-1 + Ceftri promoted greater expression levels of mucosal barrier-related proteins [KI67, MUC2, ZO-1, secretory immunoglobulin A (slgA), Clauding-1, and Occludin], better local immune responses activation, and moderately better modulation of systemic immune responses during long-term colitis. This may be due to the fact that BD-1 + Ceftri can deliberately prolong the colonization time of some beneficial microbiota (e.g., Bifidobacterium) and reduce the relative abundance of inflammation-related microbiota (e.g., Escherichia/Shigella and Ruminococcus). Interestingly, we found that the changes in the gut barrier and immunity were already present immediately after early intervention with BD-1 + Ceftri, implying that early effects can persist with appropriate intervention. Furthermore, intervention with BD-1 alone in early life confers an anti-inflammatory effect to a certain degree in the long-term, which may be due to the interaction between BD-1 and the host’s native gut microbiota affecting intestinal metabolites. In conclusion, BD-1 was not as effective as BD-1 + Ceftri in early life, perhaps due to its failure to fully play the role of the strain itself under the influence of the host’s complex microbiota. Therefore, further research is needed to explore specific mechanisms for single strain and native microbiota or the combination between probiotics and antibiotics.

Fatty Acid Homeostasis Tunes Flagellar Motility by Activating Phase 2 Flagellin Expression, Contributing to Salmonella Gut Colonization

Long-chain-fatty-acid (LCFA) metabolism is a fundamental cellular process in bacteria that is involved in lipid homeostasis, energy production, and infection. However, the role of LCFA metabolism in Salmonella enterica serovar Typhimurium (S. Tm) gut infection remains unclear. Here, using a murine gastroenteritis infection model, we demonstrate involvement of LCFA metabolism in S. Tm gut colonization. The LCFA metabolism-associated transcriptional regulator FadR contributes to S. Tm gut colonization. fadR deletion alters the gene expression profile and leads to aberrant flagellar motility of S. Tm. Colonization defects in the fadR mutant are attributable to altered swimming behavior characterized by less frequently smooth swimming, resulting from reduced expression of the phase 2 flagellin FljB. Notably, changes in lipid LCFA composition by fadR deletion lead to reduced expression of fljB, which is restored by exogenous LCFA. Therefore, LCFA homeostasis may maintain proper flagellar motility by activating fljB expression, contributing to S. Tm gut colonization. Our findings improve the understanding of the effect of luminal LCFA on the virulence of enteric pathogens.

Cecal Metabolomic Fingerprint of Unscathed Rats: Does It Reflect the Good Response to a Provocative Decompression?

On one side, decompression sickness (DCS) with neurological disorders lead to a reshuffle of the cecal metabolome of rats. On the other side, there is also a specific and different metabolomic signature in the cecum of a strain of DCS-resistant rats, that are not exposed to hyperbaric protocol. We decide to study a conventional strain of rats that resist to an accident-provoking hyperbaric exposure, and we hypothesize that the metabolomic signature put forward may correspond to a physiological response adapted to the stress induced by diving. The aim is to verify and characterize whether the cecal compounds of rats resistant to the provocative dive have a cecal metabolomic signature different from those who do not dive. 35 asymptomatic diver rats are selected to be compared to 21 rats non-exposed to the hyperbaric protocol. Because our aim is essentially to study the differences in the cecal metabolome associated with the hyperbaric exposure, about half of the rats are fed soy and the other half of maize in order to better rule out the effect of the diet itself. Lower levels of IL-1β and glutathione peroxidase (GPX) activity are registered in blood of diving rats. No blood cell mobilization is noted. Conventional and ChemRICH approaches help the metabolomic interpretation of the 185 chemical compounds analyzed in the cecal content. Statistical analysis show a panel of 102 compounds diet related. 19 are in common with the hyperbaric protocol effect. Expression of 25 compounds has changed in the cecal metabolome of rats resistant to the provocative dive suggesting an alteration of biliary acids metabolism, most likely through actions on gut microbiota. There seem to be also weak changes in allocations dedicated to various energy pathways, including hormonal reshuffle. Some of the metabolites may also have a role in regulating inflammation, while some may be consumed for the benefit of oxidative stress management.

Microbial Imbalance Induces Inflammation by Promoting Salmonella Penetration through the Mucosal Barrier

The balance of microbial species in the intestine must be maintained to prevent inflammation and disease. Healthy bacteria suppress infection by pathogens and prevent disorders such as inflammatory bowel diseases (IBDs). The role of mucus in the relation between pathogens and the intestinal microbiota is poorly understood. Here, we hypothesized that healthy bacteria inhibit infection by preventing pathogens from penetrating the mucus layer and that microbial imbalance leads to inflammation by promoting the penetration of the mucosal barrier. We tested this hypothesis with an in vitro model that contains mucus, an epithelial cell layer, and resident immune cells. We found that, unlike probiotic VSL#3 bacteria, Salmonella penetrated the mucosal layers and induced the production of interleukin-8 (IL-8) and tumor necrosis factor (TNF)-α. At ratios greater than 10⁴:1, probiotic bacteria suppressed the growth and penetration of Salmonella and reduced the production of inflammatory cytokines. Counterintuitively, low densities of healthy bacteria increased both pathogen penetration and cytokine production. In all cases, mucus increased Salmonella penetration and the production of cytokines. These results suggest that mucus lessens the protective effect of probiotic bacteria by promoting barrier penetration. In this model, a more imbalanced microbial population caused infection and inflammation by selecting pathogens that are more invasive and immunogenic. Combined, the results suggest that the depletion of commensal bacteria or an insufficient dosage of probiotics could worsen an infection and cause increased inflammation. A better understanding of the interactions between pathogens, healthy microbes, and the mucosal barrier will improve the treatment of infections and inflammatory diseases.

Dynamics of Microbial Communities across the Life Stages of Nilaparvata lugens (Stål)

Understanding the composition of microorganismal communities hosted by insect pests is an important prerequisite for revealing their functions and developing new pest control strategies. Although studies of the structure of the microbiome of Nilaparvata lugens have been published, little is known about the dynamic changes in this microbiome across different developmental stages, and an understanding of the core microbiota is still lacking. In this study, we investigated the dynamic changes in bacteria and fungi in different developmental stages of N. lugens using high-throughput sequencing technology. We observed that the microbial diversity in eggs and mated adults was higher than that in nymphs and unmated adults. We also observed a notable strong correlation between fungal and bacterial α-diversity, which suggests that fungi and bacteria are closely linked and may perform functions collaboratively during the whole developmental period. Arsenophonus and Hirsutella were the predominant bacterial and fungal taxa, respectively. Bacteria were more conserved than fungi during the transmission of the microbiota between developmental stages. Compared with that in the nymph and unmated adult stages of N. lugens, the correlation between bacterial and fungal communities in the mated adult and egg stages was stronger. Moreover, the core microbiota across all developmental stages in N. lugens was identified, and there were more bacterial genera than fungal genera; notably, the core microbiota of eggs, nymphs, and mated and unmated adults showed distinctive functional enrichment. These findings highlight the potential value of further exploring microbial functions during different developmental stages and developing new pest management strategies.

Moniezia benedeni Infection Restrain IgA+, IgG+, and IgM+ Cells Residence in Sheep (Ovis aries) Small Intestine

Secreted immunoglobulin A (SIgA), IgG, and IgM play a crucial role in forming the intestinal mucosal immune barrier, and parasites could disturb the host's immune response by releasing various immunomodulatory molecules. Moniezia benedeni is an important pathogen parasitizing in the sheep small intestine. It is aimed to explore the residence characteristics of IgA⁺, IgG⁺, and IgM⁺ cells in the sheep small intestine, and the influence of Moniezia benedeni infection on them. Control group (n = 6) and infected group (n = 6) were selected, respectively, and the three subtype cells residing in the small intestine were systematically observed and analyzed. The results showed that in the Control group, the three types of positive cells were all distributed diffusely, and the total densities in jejunum, duodenum and ileum was gradually declined in turn. Notably, the change trend of IgA⁺ and IgG⁺ cells densities were both congruent with the total densities, and the differences among them were significant, respectively (P < 0.05); the IgM⁺ cells density was the highest in duodenum, followed by jejunum and ileum, there was no significant difference between duodenum and jejunum (P > 0.05), but both significantly higher than in ileum (P < 0.05). In the Infected group, their total densities in duodenum, jejunum and ileum were gradually declined in turn. Notably, the IgA⁺ and IgM⁺ cells densities change trend was the same as the total densities, and the differences among them were significant, respectively (P < 0.05). The IgG⁺ cells density in duodenum was the highest, followed by ileum and jejunum and there was significantly difference among them (P < 0.05). The comparison results between Control and Infected groups showed that from the duodenum, jejunum to ileum, IgA⁺, IgG⁺, and IgM⁺ cells were all reduced significantly, respectively. The results suggest that the three types of positive cells were resided heterogeneously in the small intestinal mucosa, that is, significant region-specificity; Moniezia benedeni infection could not change their diffuse distribution characteristics, but strikingly, reduce their resident densities, and the forming mucosal immune barrier were significantly inhibited. It provided powerful evidence for studying on the molecular mechanism of Moniezia benedeni evasion from immune surveillance by strongly inhibiting the host's mucosal immune barrier.

The Game for Three: Salmonella–Host–Microbiota Interaction Models

Colonization of the gastrointestinal (GI) tract by enteric pathogens occurs in a context strongly determined by host-specific gut microbiota, which can significantly affect the outcome of infection. The complex gameplay between the trillions of microbes that inhabit the GI tract, the host, and the infecting pathogen defines a specific triangle of interaction; therefore, a complete model of infection should consider all of these elements. Many different infection models have been developed to explain the complexity of these interactions. This review sheds light on current knowledge, along with the strengths and limitations of in vitro and in vivo models utilized in the study of Salmonella–host–microbiome interactions. These models range from the simplest experiment simulating environmental conditions using dedicated growth media through in vitro interaction with cell lines and 3-D organoid structure, and sophisticated “gut on a chip” systems, ending in various animal models. Finally, the challenges facing this field of research and the important future directions are outlined.

Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium

Intestinal inflammation fuels the transmission of Salmonella Typhimurium (S.Tm). However, a substantial fitness cost is associated with virulence expression. Mutations inactivating transcriptional virulence regulators generate attenuated variants profiting from inflammation without enduring virulence cost. Such variants interfere with the transmission of fully virulent clones. Horizontal transfer of functional regulatory genes (HGT) into attenuated variants could nevertheless favor virulence evolution. To address this hypothesis, we cloned hilD, coding for the master regulator of virulence, into a conjugative plasmid that is highly transferrable during intestinal colonization. The resulting mobile hilD allele allows virulence to emerge from avirulent populations, and to be restored in attenuated mutants competing against virulent clones within-host. However, mutations inactivating the mobile hilD allele quickly arise. The stability of virulence mediated by HGT is strongly limited by its cost, which depends on the hilD expression level, and by the timing of transmission. We conclude that robust evolution of costly virulence expression requires additional selective forces such as narrow population bottlenecks during transmission.

Salmonella Typhimurium virulence is costly and can be lost by mutation during infection. Bakkeren et al. show that virulence restoration via horizontal gene transfer is only transient while transmission bottlenecks promote long-term virulence stability.

Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development

Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.

Dietary supplementation with low-dose xylooligosaccharide promotes the anti-Salmonella activity of probiotic Lactiplantibacillus plantarum ZS2058 in a murine model

Oligosaccharides have been previously reported to cause an aggravation of Salmonella infection. In this study, we reduced the dietary supplementation of oligosaccharides (1% w/w) and studied their effects on the anti-Salmonella activity of probiotic Lactiplantibacillus plantarum (L. plantarum) ZS2058. The results showed that among all five studied oligosaccharides, only xylooligosaccharide (XOS) promoted the anti-Salmonella activity of L. plantarum ZS2058 by increasing the survival rate of the infected mice (66.7% vs. 53.3%). Further study revealed that XOS did not function synergistically with L. plantarum ZS2058, as XOS itself did not improve the survival rate of the infected mice. In an in vitro coculture system, XOS significantly promoted the antagonistic activity (92% increase) of L. plantarum ZS2058 against Salmonella. In Salmonella-infected mice, the combination of XOS and L. plantarum ZS2058 significantly increased the faecal content of short-chain fatty acids (SCFAs) and restored the production of proinflammatory cytokines. More importantly, XOS, L. plantarum ZS2058 and their combination changed the gut microbiota into distinct profiles. Linear Discriminant Analysis (LDA) effect size (LEfSe) analysis identified five taxa as marker bacteria for mice treated with a combination of XOS and L. plantarum ZS2058. In particular, Mucispirillum, which was previously reported to protect the host from Salmonella infection, was increased. Here, we showed that low dose XOS could promote the anti-Salmonella activity of the probiotic L. plantarum ZS2058. These results offer new opportunities to cope with this predominant food-borne pathogen with great efficiency and to lay a foundation for developing functional foods with anti-Salmonella potential.

Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

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

Effects of obesity and weight-loss surgery shift the microbiome and impact alloimmune responses

PURPOSE OF REVIEW

Obesity is a worldwide health problem with increasing rates in both children and adults. Bariatric surgery (BS) represents the only effective long-term treatment. Beneficial effects of BS may be mediated through shifts of the gut microbiome. Here, we introduce data linking the microbiome to alloimmune responses.

RECENT FINDINGS

The rapid development of microbiome sequencing technologies in addition to the availability of gnotobiotic facilities have enabled mechanistic investigations on modulations of alloimmune responses through microbiomes. BS has been shown to improve comorbidities and chronic inflammation caused by obesity. Changes in microbiota and microbiota-related metabolites may play a role. Patients either listed or having received a transplant have undergone weight loss surgery, thus allowing to dissect mechanisms of microbial shifts to alloimmunity.

SUMMARY

Weight loss and BS have the potential to improve transplant outcomes by ameliorating alloimmune responses. Those effects may be carried out through alterations of the gut microbiome.

Enhancing Human Superorganism Ecosystem Resilience by Holistically ‘Managing Our Microbes’

Microbes in the 21st century are understood as symbionts ‘completing’ the human ‘superorganism’ (Homo sapiens plus microbial partners-in-health). This paper addresses a significant paradox: despite the vast majority of our genes being microbial, the lack of routine safety testing for the microbiome has led to unintended collateral side effects from pharmaceuticals that can damage the microbiome and inhibit innate ‘colonization resistance’ against pathobionts. Examples are discussed in which a Microbiome First Medicine approach provides opportunities to ‘manage our microbes’ holistically, repair dysbiotic superorganisms, and restore health and resilience in the gut and throughout the body: namely, managing nosocomial infections for Clostridioides difficile and Staphylococcus aureus and managing the gut and neural systems (gut–brain axis) in autism spectrum disorder. We then introduce a risk analysis tool: the evidence map. This ‘mapping’ tool was recently applied by us to evaluate evidence for benefits, risks, and uncertainties pertaining to the breastmilk ecosystem. Here, we discuss the potential role of the evidence map as a risk analysis methodology to guide scientific and societal efforts to: (1) enhance ecosystem resilience, (2) ‘manage our microbes’, and (3) minimize the adverse effects of both acute and chronic diseases.

Effects of Lactic Acid Bacteria Isolated from Equine on Salmonella-Infected Gut Mouse Model

The aim of this study was to evaluate the antibacterial potential of lactic acid bacteria (Weissella confuse, Pediococcus acidilactici, and Ligilactobacillus equi) isolated from healthy equine in Wuhan against Salmonella Typhimurium CVCC542-induced mice model on intestinal microflora. In previous studies, these isolated strains showed good probiotic potentials in vitro. In this study, fifty healthy mice were randomly divided into five groups, the blank control group, the control group, the Pediococcus acidilactici group (1 × 10⁸ CFU/day), the Ligilactobacillus equi group (1 × 10⁸ CFU/day), and the Weissella confuse group (1 × 10⁸ CFU/day). The body weight in control group and Weissella confuse group showed significant decreased (P < 0.05, P < 0.01), while Pediococcus acidilactici group and Ligilactobacillus equi group showed good recovering after treatments. The lowest diarrhea rate was shown in Ligilactobacillus equi group after treatment. In histopathology, Ligilactobacillus equi group showed the least structural damage in duodenum, and all probiotic treatment groups showed less damage in cecum. The sequence data and optical transform unit showed that Pediococcus acidilactici group and Ligilactobacillus equi group had higher number than control group, while the diversity data showed that the control group and Weissella confuse group had lower diversity in cecum. Microbial community analysis showed increased abundance of Firmicutes, Bacteroidetes, uncultured_bacterium_f_Muribaculaceae, and Lactobacillus in treatment groups, while potential microbes that can induce intestinal diseases such as Verrucomicrobia, Akkermansia, and Lachnospiraceae_NK4A136_group decreased in the treatment groups. In conclusion, lactic acid bacteria isolated from the healthy horses could alleviate the infection of Salmonella and regulate intestinal flora.

Glyphosate exposure disturbs the bacterial endosymbiont community and reduces body weight of the predatory ladybird beetle Harmonia axyridis (Coleoptera: Coccinellidae)

The predatory ladybird beetle, Harmonia axyridis, is a predominant natural enemy of pest insects in cotton fields. Commercialization of genetically modified crops has promoted the increased use of the herbicide glyphosate. In this study, to assess potential negative effects of glyphosate on beneficial non-target organisms in cotton fields, we first examined how glyphosate exposure affected the development and endosymbiotic bacterial community of H. axyridis. The results showed that the survival rate, development duration, pupation rate and emergence rate of H. axyridis under low and high concentrations of glyphosate exposure were not significantly changed, but glyphosate did significantly reduce the body weight of H. axyridis. Based on 16S rRNA sequencing, there were no significant differences in the diversity or richness of the endosymbiotic bacteria of H. axyridis before and after glyphosate exposure. The dominant bacterial phyla Firmicutes and Proteobacteria and genera Staphylococcus and Enterobacter remained the same regardless of treatment with glyphosate, however the abundance and copy number of these bacteria were altered. Glyphosate treatment significantly reduced the abundance and gene copy number of Staphylococcus and increased the abundance and gene copy number of Enterobacter. This is the first report demonstrating that glyphosate can reduce the body weight H. axyridis and alter the bacterial endosymbiont community by affecting the abundance and gene copy number of dominant bacteria.

Immunoglobulin A, an Active Liaison for Host-Microbiota Homeostasis

Mucosal surfaces in the gastrointestinal tract are continually exposed to native, commensal antigens and susceptible to foreign, infectious antigens. Immunoglobulin A (IgA) provides dual humoral responses that create a symbiotic environment for the resident gut microbiota and prevent the invasion of enteric pathogens. This review features recent immunological and microbial studies that elucidate the underlying IgA and microbiota-dependent mechanisms for mutualism at physiological conditions. IgA derailment and concurrent microbiota instability in pathological diseases are also discussed in detail. Highlights of this review underscore that the source of IgA and its structural form can dictate microbiota reactivity to sustain a diverse niche where both host and bacteria benefit. Other important studies emphasize IgA insufficiency can result in the bloom of opportunistic pathogens that encroach the intestinal epithelia and disseminate into circulation. The continual growth of knowledge in these subjects can lead to the development of therapeutics targeting IgA and/or the microbiota to treat life threatening diseases.

A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants

The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance¹. However, not all variants are equally fit in all environments^2,3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here, we demonstrate this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: a long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase variation^4,5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen-specific immunoglobulin A and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of rationally designed oral vaccines, we induced immunoglobulin A responses blocking all of these trajectories. This selected for Salmonella mutants carrying deletions of the O-antigen polymerase gene wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents or complement) and predation (bacteriophages) and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.

Consideration of Gut Microbiome in Murine Models of Diseases

The gut microbiome (GM), a complex community of bacteria, viruses, protozoa, and fungi located in the gut of humans and animals, plays significant roles in host health and disease. Animal models are widely used to investigate human diseases in biomedical research and the GM within animal models can change due to the impact of many factors, such as the vendor, husbandry, and environment. Notably, variations in GM can contribute to differences in disease model phenotypes, which can result in poor reproducibility in biomedical research. Variation in the gut microbiome can also impact the translatability of animal models. For example, standard lab mice have different pathogen exposure experiences when compared to wild or pet store mice. As humans have antigen experiences that are more similar to the latter, the use of lab mice with more simplified microbiomes may not yield optimally translatable data. Additionally, the literature describes many methods to manipulate the GM and differences between these methods can also result in differing interpretations of outcomes measures. In this review, we focus on the GM as a potential contributor to the poor reproducibility and translatability of mouse models of disease. First, we summarize the important role of GM in host disease and health through different gut–organ axes and the close association between GM and disease susceptibility through colonization resistance, immune response, and metabolic pathways. Then, we focus on the variation in the microbiome in mouse models of disease and address how this variation can potentially impact disease phenotypes and subsequently influence research reproducibility and translatability. We also discuss the variations between genetic substrains as potential factors that cause poor reproducibility via their effects on the microbiome. In addition, we discuss the utility of complex microbiomes in prospective studies and how manipulation of the GM through differing transfer methods can impact model phenotypes. Lastly, we emphasize the need to explore appropriate methods of GM characterization and manipulation.

Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils

BACKGROUND

Bioaugmentation aims to use the capacities of specific bacterial strains inoculated into sites to enhance pollutant biodegradation. Bioaugmentation results have been mixed, which has been attributed to poor inoculant growth and survival in the field, and, consequently, moderate catalytic performance. However, our understanding of biodegradation activity mostly comes from experiments conducted under laboratory conditions, and the processes occurring during adaptation and invasion of inoculants into complex environmental microbiomes remain poorly known. The main aim of this work was thus to study the specific and different cellular reactions of an inoculant for bioaugmentation during adaptation, growth and survival in natural clean and contaminated non-sterile soils, in order to better understand factors limiting bioaugmentation.

RESULTS

As inoculant we focused on the monoaromatic compound-degrading bacterium Pseudomonas veronii 1YdBTEX2. The strain proliferated in all but one soil types in presence and in absence of exogenously added toluene. RNAseq and differential genome-wide gene expression analysis illustrated both a range of common soil responses such as increased nutrient scavenging and recycling, expression of defense mechanisms, as well as environment-specific reactions, notably osmoprotection and metal homeostasis. The core metabolism of P. veronii remained remarkably constant during exponential growth irrespective of the environment, with slight changes in cofactor regeneration pathways, possibly needed for balancing defense reactions.

CONCLUSIONS

P. veronii displayed a versatile global program, enabling it to adapt to a variety of soil environments in the presence and even in absence of its target pollutant toluene. Our results thus challenge the widely perceived dogma of poor survival and growth of exogenous inoculants in complex microbial ecosystems such as soil and provide a further basis to developing successful bioaugmentation strategies.

Western-style diet impedes colonization and clearance of Citrobacter rodentium

Western-style diet (WSD), which is high in fat and low in fiber, lacks nutrients to support gut microbiota. Consequently, WSD reduces microbiota density and promotes microbiota encroachment, potentially influencing colonization resistance, immune system readiness, and thus host defense against pathogenic bacteria. Here we examined the impact of WSD on infection and colitis in response to Citrobacter rodentium. We observed that, relative to mice consuming standard rodent grain-based chow (GBC), feeding WSD starkly altered the dynamics of Citrobacter infection, reducing initial colonization and inflammation but frequently resulting in persistent infection that associated with low-grade inflammation and insulin resistance. WSD's reduction in initial Citrobacter virulence appeared to reflect that colons of GBC-fed mice contain microbiota metabolites, including short-chain fatty acids, especially acetate, that drive Citrobacter growth and virulence. Citrobacter persistence in WSD-fed mice reflected inability of resident microbiota to out-compete it from the gut lumen, likely reflecting the profound impacts of WSD on microbiota composition. These studies demonstrate potential of altering microbiota and their metabolites by diet to impact the course and consequence of infection following exposure to a gut pathogen.

Establishing causality in Salmonella-microbiota-host interaction: The use of gnotobiotic mouse models and synthetic microbial communities

Colonization resistance (CR), the ability to block infections by potentially harmful microbes, is a fundamental function of host-associated microbial communities and highly conserved between animals and humans. Environmental factors such as antibiotics and diet can disturb microbial community composition and thereby predispose to opportunistic infections. The most prominent is Clostridioides difficile, the causative agent of diarrhea and pseudomembranous colitis. In addition, the risk to succumb to infections with genuine human enteric pathogens like nontyphoidal Salmonella (NTS) is also increased by a low-diverse, diet or antibiotic-disrupted microbiota. Despite extensive microbial community profiling efforts, only a limited set of microorganisms have been causally linked with protection against enteric pathogens. Furthermore, it remains a challenge to predict colonization resistance from complex microbiome signatures due to context-dependent action of microorganisms. In the past decade, the study of NTS infection has led to the description of several fundamental principles of microbiota-host-pathogen interaction. In this review, I will give an overview on the current state of knowledge in this field and outline experimental approaches to gain functional insight to the role of specific microbes, functions and metabolites in Salmonella-microbiota-host interaction. In particular, I will highlight the value of mouse infection models, which, in combination with culture collections, synthetic communities and gnotobiotic models have become essential tools to screen for protective members of the microbiota and establishing causal relationship and mechanisms in infection research.

Aging, Frailty, and the Microbiome-How Dysbiosis Influences Human Aging and Disease

The human gut microbiome is a collection of bacteria, protozoa, fungi, and viruses that coexist in our bodies and are essential in protective, metabolic, and physiologic functions of human health. Gut dysbiosis has traditionally been linked to increased risk of infection, but imbalances within the intestinal microbial community structure that correlate with untoward inflammatory responses are increasingly recognized as being involved in disease processes that affect many organ systems in the body. Furthermore, it is becoming more apparent that the connection between gut dysbiosis and age-related diseases may lie in how the gut microbiome communicates with both the intestinal mucosa and the systemic immune system, given that these networks have a common interconnection to frailty. We therefore discuss recent advances in our understanding of the important role the microbiome plays in aging and how this knowledge opens the door for potential novel therapeutics aimed at shaping a less dysbiotic microbiome to prevent or treat age-related diseases.