Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

Distinct gut bacterial composition in Anoplophora glabripennis reared on two host plants

Anoplophora glabripennis (Coleoptera: Cerambycidae: Lamiinae) is an invasive wood borer pest that has caused considerable damage to forests. Gut bacteria are of great importance in the biology and ecology of herbivores, especially in growth and adaptation; however, change in the gut bacterial community of this pest feeding on different hosts is largely unknown. In this study, we investigated the gut bacterial communities of A. glabripennis larvae fed on different preferred hosts, Salix matsudana and Ulmus pumila, using 16S rDNA high-throughput sequencing technology. A total of 15 phyla, 25 classes, 65 orders, 114 families, 188 genera, and 170 species were annotated in the gut of A. glabripennis larvae fed on S. matsudana or U. pumila using a 97% similarity cutoff level. The dominant phyla were Firmicutes and Proteobacteria and the core dominant genera were Enterococcus, Gibbsiella, Citrobacter, Enterobacter, and Klebsiella. There was significantly higher alpha diversity in the U. pumila group than in the S. matsudana group, and principal co-ordinate analysis showed significant differences in gut bacterial communities between the two groups. The genera with significant abundance differences between the two groups were Gibbsiella, Enterobacter, Leuconostoc, Rhodobacter, TM7a, norank, Rhodobacter, and Aurantisolimonas, indicating that the abundance of larval gut bacteria was affected by feeding on different hosts. Further network diagrams showed that the complexity of the network structure and the modularity were higher in the U. pumila group than in the S. matsudana group, suggesting more diverse gut bacteria in the U. pumila group. The dominant role of most gut microbiota was related to fermentation and chemoheterotrophy, and specific OTUs positively correlated with different functions were reported. Our study provides an essential resource for the gut bacteria functional study of A. glabripennis associated with host diet.

Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas

Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June 2018 and May 2019. In the top-down approach used in this study, we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2,167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole-genome sequencing analytical methodologies (core genome multilocus sequence typing [cgMLST], core single nucleotide polymorphism [coreSNP] analysis, and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequence types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium. IMPORTANCE Enterococcus faecium is a member of the gastrointestinal microbiota. Although its virulence is low in healthy, immunocompetent individuals, E. faecium has become the third leading cause of health care-associated infections in the United States. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from cancer patients at the University of Arkansas for Medical Sciences (UAMS). We employed a top-down analytical approach (from population genomics to molecular biology) to classify our clinical isolates into their genetic lineages and thoroughly evaluate their antibiotic resistance and virulence profiles. The addition of patient epidemiological data to the whole-genome sequencing analytical methodologies performed in the study allowed us to increase our understanding of the relationships and transmission dynamics of the E. faecium isolates. This study provides new insights into genomic surveillance of E. faecium to help monitor and further limit the spread of multidrug-resistant E. faecium.

Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives

Microbial community in natural or artificial environments playes critical roles in substance cycles, products synthesis and species evolution. Although microbial community structures have been revealed via culture-dependent and culture-independent approaches, the hidden forces driving the microbial community are rarely systematically discussed. As a mode of cell-to-cell communication that modifies microbial interactions, quorum sensing can regulate biofilm formation, public goods secretion, and antimicrobial substances synthesis, directly or indirectly influencing microbial community to adapt to the changing environment. Therefore, the current review focuses on microbial community in the different habitats from the quorum sensing perspective. Firstly, the definition and classification of quorum sensing were simply introduced. Subsequently, the relationships between quorum sensing and microbial interactions were deeply explored. The latest progressives regarding the applications of quorum sensing in wastewater treatment, human health, food fermentation, and synthetic biology were summarized in detail. Finally, the bottlenecks and outlooks of quorum sensing driving microbial community were adequately discussed. To our knowledge, this current review is the first to reveal the driving force of microbial community from the quorum sensing perspective. Hopefully, this review provides a theoretical basis for developing effective and convenient approaches to control the microbial community with quorum sensing approaches.

Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium

The human gut is home to trillions of microorganisms that influence several aspects of our health. This dense microbial community targets almost all dietary polysaccharides and releases multiple metabolites, some of which have physiological effects on the host. A healthy equilibrium between members of the gut microbiota, its microbial diversity, and their metabolites is required for intestinal health, promoting regulatory or anti-inflammatory immune responses. In contrast, the loss of this equilibrium due to antibiotics, low fiber intake, or other conditions results in alterations in gut microbiota composition, a term known as gut dysbiosis. This dysbiosis can be characterized by a reduction in health-associated microorganisms, such as butyrate-producing bacteria, enrichment of a small number of opportunistic pathogens, or a reduction in microbial diversity. Bifidobacterium species are key species in the gut microbiome, serving as primary degraders and contributing to a balanced gut environment in various ways. Colonization resistance is a fundamental property of gut microbiota for the prevention and control of infections. This community competes strongly with foreign microorganisms, such as gastrointestinal pathogens, antibiotic-resistant bacteria, or even probiotics. Resistance to colonization is based on microbial interactions such as metabolic cross-feeding, competition for nutrients, or antimicrobial-based inhibition. These interactions are mediated by metabolites and metabolic pathways, representing the inner workings of the gut microbiota, and play a protective role through colonization resistance. This review presents a rationale for how microbial interactions provide resistance to colonization and gut dysbiosis, highlighting the protective role of Bifidobacterium species.

Butyrate driven raft disruption trots off enteric pathogen invasion: possible mechanism of colonization resistance

The gut microbiome derived short chain fatty acids perform multitude of functions to maintain gut homeostasis. Here we studied how butyrate stymie enteric bacterial invasion in cell using a simplistic binary model. The surface of the mammalian cells is enriched with microdomains rich in cholesterol that are known as rafts and act as entry points for pathogens. We showed that sodium butyrate treated RAW264.7 cells displayed reduced membrane cholesterol and less cholera-toxin B binding coupled with increased membrane fluidity compared to untreated cells indicating that reduced membrane cholesterol caused disruption of lipid rafts. The implication of such cellular biophysical changes on the invasion of enteric pathogenic bacteria was assessed. Our study showed, in comparison to untreated cells, butyrate-treated cells significantly reduced the invasion of Shigella and Salmonella, and these effects were found to be reversed by liposomal cholesterol treatment, increasing the likelihood that the rafts' function against bacterial invasion. The credence of ex vivo studies found to be in concordance in butyrate fed mouse model as evident from the significant drift towards a protective phenotype against virulent enteric pathogen invasion as compared to untreated mice. To produce a cytokine balance towards anti-inflammation, butyrate-treated mice produced more of the gut tissue anti-inflammatory cytokine IL-10 and less of the pro-inflammatory cytokines TNF-α, IL-6, and IFN-γ. In histological studies of Shigella infected gut revealed a startling observation where number of neutrophils infiltration was noted which was correlated with the pathology and was essentially reversed by butyrate treatment. Our results ratchet up a new dimension of our understanding how butyrate imparts resistance to pathogen invasion in the gut.

Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming

Fusobacterium nucleatum (Fn) and enterotoxigenic Bacteroides fragilis (ETBF) are two pathobionts consistently enriched in the gut microbiomes of patients with colorectal cancer (CRC) compared to healthy counterparts and frequently observed for their direct association within tumors. Although several molecular mechanisms have been identified that directly link these organisms to features of CRC in specific cell types, their specific effects on the epithelium and local immune compartment are not well-understood. To fill this gap, we leveraged single-cell RNA sequencing (scRNA-seq) on wildtype mice and mouse model of CRC. We find that Fn and ETBF exacerbate cancer-like transcriptional phenotypes in transit-amplifying and mature enterocytes in a mouse model of CRC. We also observed increased T cells in the pathobiont-exposed mice, but these pathobiont-specific differences observed in wildtype mice were abrogated in the mouse model of CRC. Although there are similarities in the responses provoked by each organism, we find pathobiont-specific effects in Myc-signaling and fatty acid metabolism. These findings support a role for Fn and ETBF in potentiating tumorigenesis via the induction of a cancer stem cell-like transit-amplifying and enterocyte population and the disruption of CTL cytotoxic function.

Impact of childhood malnutrition and intestinal microbiota on MDR infections

The global burden of infection from MDR organisms (MDROs) disproportionately affects children residing in low- and middle-income countries and those with increased healthcare exposure. These populations have high rates of malnutrition making them increasingly vulnerable to infection with intestinal-derived pathogens. Malnourished children experience increased incidence of intestinal carriage and invasive infection with intestinal-derived MDROs including ESBL- and carbapenemase-producing Enterobacterales. However, the relationship between malnutrition and MDRO infection remains to be clearly defined. Impairment in intestinal barrier function and innate and adaptive immunity in malnutrition increases the risk for infection with intestinal-derived pathogens, and there is an increasing appreciation of the role of the intestinal microbiota in this process. Current evidence from human studies and animal models suggests that diet and the intestinal microbiota influence each other to determine nutritional status, with important implications for infectious outcomes. These insights are crucial to developing microbiota-targeted strategies aimed at reversing the growing burden of MDRO infections in malnourished populations worldwide.

Microbial profiles and immune responses in seahorse gut and brood pouch under chronic exposure to environmental antibiotics

Ocean antibiotics pose substantial risks to the adaptation and lifespan of marine organisms. Seahorses are unique owing to the occurrence of brood pouches, male pregnancy, and loss of gut-associated lymphatic tissues and spleen, which lead to increased sensitivity to environmental changes. This study evaluated the changes in microbial diversity and immune responses within the gut and brood pouch in the lined seahorse Hippocampus erectus under chronic exposure to environmental levels of triclosan (TCS) and sulfamethoxazole (SMX), which are common antibiotics in coastal regions. The results showed that microbial abundance and diversity within the gut and brood pouch of seahorses were significantly changed following antibiotics treatment, with the expression of core genes involved in immunity, metabolism, and circadian rhythm processes evidently regulated. Notably, the abundance of potential pathogens in brood pouches was considerably increased upon treatment with SMX. Transcriptome analysis revealed that the expression of toll-like receptors, c-type lectins, and inflammatory cytokine genes in brood pouches was significantly upregulated. Notably, some essential genes related to male pregnancy significantly varied after antibiotic treatment, implying potential effects on seahorse reproduction. This study provides insights into the physiological adaptation of marine animals to environmental changes resulting from human activity.

P2X7 Receptor Modulation of the Gut Microbiota and the Inflammasome Determines the Severity of Toxoplasma gondii-Induced Ileitis

In mice, oral Toxoplasma gondii infection induces severe ileitis. The aim of the present study was to investigate the impact of the P2X7 receptor (P2X7) on the inflammatory response to T. gondii-induced ileitis. Cysts of the ME49 strain of T. gondii were used to induce ileitis. The infected mice were euthanized on day 8 and ileal tissue and peripheral blood were collected for histopathological and immunohistochemical analyses. Ileal contractility, inflammatory mediators, inflammasome activation, quantitative PCR analysis of gene expression, and fecal microbiota were assessed using appropriate techniques, respectively. The infected P2X7-/- mice had greater disease severity, parasitic burden, liver damage, and intestinal contractility than the infected wild-type (WT) mice. Infection increased serum IL-6 and IFN-γ and tissue caspase-1 but not NLRP3 in P2X7-/- mice compared to WT mice. Bacteroidaceae, Rikenellaceae, and Rhodospirillales increased while Muribaculaceae and Lactobacillaceae decreased in the infected WT and P2X7-/- mice. Bacteroidia and Tannerellaceae increased in the P2X7-/- mice with ileitis. By contrast, Clostridiales and Mollicutes were absent in the P2X7-/- mice but increased in the WT mice. P2X7 protects mice against T. gondii infection by activating the inflammasome and regulating the local and systemic immune responses. Specific gut bacterial populations modulated by P2X7 determine disease severity.

Cutaneous Surgical Wounds Have Distinct Microbiomes from Intact Skin

Infections are relatively rare following cutaneous surgical procedures, despite the potential for wound exposure to pathogens both during surgery and throughout the healing process. Although gut commensals are believed to reduce the risk of intestinal infections, an analogous role for skin commensals has not been described. In fact, the microbiome of normally healing surgical skin wounds has not yet been profiled using culture-independent techniques. We characterized the wound microbiome in 53 patients who underwent skin cancer surgery and healed without signs or symptoms of infection. A week after surgery, several bacterial species displayed significant differences in relative abundance when compared to control, nonoperated skin from the same patient. The relative abundance of the most common bacterium found on intact skin, Cutibacterium acnes, was reduced in wounds 5-fold. Staphylococcus aureus, a frequent cause of postoperative skin infections, was enriched 6.4-fold in clinically noninfected wounds, suggesting active suppression of pathogenicity. Finally, members of the Corynebacterium genus were the dominant organism in postoperative wounds, making up 37% of the average wound microbiome. The enrichment of these bacteria in normally healing wounds suggests that they might be capable of providing colonization resistance. Future studies focused on the biological and clinical significance of the wound microbiome may shed light on normal wound healing and potential therapeutic opportunities to mitigate infection risk. IMPORTANCE Commensal bacteria on skin may limit the ability of pathogenic bacteria to cause clinically significant infections. The bacteria on healing acute wounds, which might provide such a protective effect, have not been described using culture-independent approaches in the absence of antibiotics. We compare the microbiome of wounds a week after skin cancer removal surgery with intact skin from the same patient. We find that the potentially pathogenic species S. aureus is common on these healing wounds despite the absence of symptoms or signs of infection. We report that bacteria often considered as potential skin probiotics, including Staphylococcus epidermidis, do not reach high relative abundance in wound microbiomes. In contrast, specific members of the Corynebacterium genus, rarely associated with infections, were significantly enriched in healing wounds compared to intact skin. Future work is needed to see if Corynebacterium species or derivatives thereof could be employed to lower the risk of wound infection.

Evolving interplay between natural products and gut microbiota

Growing evidence suggests gut microbiota status affects human health, and microbiota imbalance will induce multiple disorders. Natural products are gaining increasing attention for their therapeutical effects and less side effects. The emerging studies support that the activities of many natural products are dependent on gut microbiota, meanwhile gut microbiota is modulated by natural products. In this review, we summarized the interplay between the gut microbiota and host disease, and the emerging molecular mechanisms of the interaction between natural products and gut microbiota. Focusing on gut microbiota metabolite of various natural products, and the effects of natural products on gut microbiota, we summarized the biotransformation pathways of natural products, and discussed the effect of natural products on the composition modulation of gut microbiota, protection of gut mucosal barrier and modulation of the gut microbiota metabolites. Dissecting the interplay between gut microbiota and natural products will help elucidate the therapeutic mechanisms of natural products.

Host-microbiota interactions and responses of Metapenaeus ensis infected with decapod iridescent virus 1

Introduction

Decapod iridescent virus 1 (DIV1) has caused severe economic losses in shrimp aquaculture. So far, Researchs on DIV1-infected shrimp have mainly focused on the hemocytes immune response, while studies on the host-intestine microbiota interactions during DIV1 infection have been scarce.

Methods

This study determined the lethal concentration 50 (LC₅₀) of DIV1 to Metapenaeus ensis, preliminarily determining that M. ensis could serve as a susceptible object for DIV1. The interactions and responses between the immune and intestine microbiota of shrimp under DIV1 infection were also investigated.

Results and Discussion

DIV1 infection decreases intestine bacterial diversity and alters the composition of intestine microbiota. Specifically, DIV1 infection decreases the abundance of potentially beneficial bacteria (Bacteroidetes, Firmicutes, and Actinobacteria), and significantly increases the abundance of pathogenic bacteria such as Vibrio and Photobacterium, thereby increasing the risk of secondary bacterial infections. The results of PICRUSt functional prediction showed that altered intestine microbiota induces host metabolism disorders, which could be attributed to the bioenergetic and biosynthetic requirements for DIV1 replication in shrimp. The comparative transcriptomic analysis showed that some metabolic pathways related to host immunity were significantly activated following DIV1 infection, including ncRNA processing and metabolic process, Ascorbate and aldarate metabolism, and Arachidonic acid metabolism. M. ensis may against DIV1 infection by enhancing the expression of some immune-related genes, such as Wnt16, heat shock protein 90 (Hsp90) and C-type lectin 3 (Ctl3). Notably, correlation analysis of intestinal microbial variation with host immunity showed that expansion of pathogenic bacteria (Vibrio and Photobacterium) in DIV1 infection could increased the expression of NF-κB inhibitors cactus-like and Toll interacting protein (Tollip), which may limit the TLR-mediated immune response and ultimately lead to further DIV1 infection.

Significance and Impact of the Study

This study enhances our understanding of the interactions between shrimp immunity and intestinal microbiota. The ultimate goal is to develop novel immune enhancers for shrimp and formulate a safe and effective DIV1 defense strategy.

Dose-Related Regulatory Effect of Raspberry Polyphenolic Extract on Cecal Microbiota Activity, Lipid Metabolism and Inflammation in Rats Fed a Diet Rich in Saturated Fats

The amount of berry polyphenols required to exert health-promoting effects seems to be difficult to achieve by fresh fruit ingestion, so polyphenol-rich extracts could be considered a dietary alternative. In the present study, laboratory rats were fed high-fat diets supplemented with 0.1 or 0.3% raspberry polyphenols from pomace, with the former dose reflecting the amount of polyphenols consumed with a glass of fresh raspberries. It was hypothesized that beneficial changes in blood and hepatic tissue related to lipid metabolism would accompany both treatments, but the health-promoting effect would be more noticeable with the higher dose of extract. This hypothesis was confirmed, and the high dose of raspberry polyphenols was better than the low dose extract in terms of decreased epididymal white adipose tissue weight, hepatic triglyceride content, PPARγ and SREBP-1c expression in the liver, and plasma IL-6 concentration, as well as increased acetic acid concentration in the cecal digesta. These effects might be partially associated with the enhanced content of ellagitannin and anthocyanin metabolites found in the blood plasma of rats administered the high dose of the extract. The results showed that this extract could be considered a dietary vehicle to provide an amount of raspberry polyphenols that could promote health.

Microencapsulation protected Lactobacillus viability and its activity in modulating the intestinal microbiota in newly weaned piglets

Lactobacilli are sensitive to heat, which limits their application as probiotics in livestock production. Lactobacillus rhamnosus LB1 was previously shown to reduce enterotoxigenic Escherichia coli (ETEC) and Salmonella infections in pigs. To investigate its potential in the application, the bacterium was microencapsulated and examined for its survival from feed pelleting and long-term storage as well as its function in modulating pig intestinal microbiota. The in vitro studies showed that freshly microencapsulated Lactobacillus rhamnosus LB1 had viable counts of 9.03 ± 0.049 log10 colony-forming units/g, of which only 0.06 and 0.87 Log of viable counts were reduced after storage at 4 and 22 °C for 427 d. The viable counts of encapsulated Lactobacillus rhamnosus LB1 were 1.06 and 1.54 Log higher in the pelleted and mash feed, respectively, than the non-encapsulated form stored at 22 °C for 30 d. In the in vivo studies, 80 piglets (weaned at 21 d of age) were allocated to five dietary treatments for a 10-d growth trial. The dietary treatments were the basal diet (CTL) and basal diet combined with either non-encapsulated LB1 (NEP), encapsulated LB1 (EP), bovine colostrum (BC), or a combination of encapsulated LB1 and bovine colostrum (EP-BC). The results demonstrated that weaning depressed feed intake and reduced growth rates in pigs of all the treatments during 21 to 25 d of age; however, the body weight gain was improved during 25 to 31 d of age in all groups with the numerically highest increase in the EP-BC-fed pigs during 21 to 31 d of age. Dietary treatments with EP, particularly in combination with BC, modulated pig intestinal microbiota, including an increase in Lactobacillus relative abundance. These results suggest that microencapsulation can protect Lactobacillus rhamnosus LB1 against cell damage from a high temperature during processing and storage and there are possible complementary effects between EP and BC.

Efficacy of Bifidobacterium longum alone or in multi-strain probiotic formulations during early life and beyond

The significance of Bifidobacterium to human health can be appreciated from its early colonization of the neonatal gut, where Bifidobacterium longum represents the most abundant species. While its relative abundance declines with age, it is further reduced in several diseases. Research into the beneficial properties of B. longum has unveiled a range of mechanisms, including the production of bioactive molecules, such as short-chain fatty acids, polysaccharides, and serine protease inhibitors. From its intestinal niche, B. longum can have far-reaching effects in the body influencing immune responses in the lungs and even skin, as well as influencing brain activity. In this review, we present the biological and clinical impacts of this species on a range of human conditions beginning in neonatal life and beyond. The available scientific evidence reveals a strong rationale for continued research and further clinical trials that investigate the ability of B. longum to treat or prevent a range of diseases across the human lifespan.

Enterohemorrhagic Escherichia coli responds to gut microbiota metabolites by altering metabolism and activating stress responses

Enterohemorrhagic Escherichia coli (EHEC) is a major cause of severe bloody diarrhea, with potentially lethal complications, such as hemolytic uremic syndrome. In humans, EHEC colonizes the colon, which is also home to a diverse community of trillions of microbes known as the gut microbiota. Although these microbes and the metabolites that they produce represent an important component of EHEC's ecological niche, little is known about how EHEC senses and responds to the presence of gut microbiota metabolites. In this study, we used a combined RNA-Seq and Tn-Seq approach to characterize EHEC's response to metabolites from an in vitro culture of 33 human gut microbiota isolates (MET-1), previously demonstrated to effectively resolve recurrent Clostridioides difficile infection in human patients. Collectively, the results revealed that EHEC adjusts to growth in the presence of microbiota metabolites in two major ways: by altering its metabolism and by activating stress responses. Metabolic adaptations to the presence of microbiota metabolites included increased expression of systems for maintaining redox balance and decreased expression of biotin biosynthesis genes, reflecting the high levels of biotin released by the microbiota into the culture medium. In addition, numerous genes related to envelope and oxidative stress responses (including cpxP, spy, soxS, yhcN, and bhsA) were upregulated during EHEC growth in a medium containing microbiota metabolites. Together, these results provide insight into the molecular mechanisms by which pathogens adapt to the presence of competing microbes in the host environment, which ultimately may enable the development of therapies to enhance colonization resistance and prevent infection.

Antibiofilm and Antivirulence Activities of Gold and Zinc Oxide Nanoparticles Synthesized from Kimchi-Isolated Leuconostoc sp. Strain C2

The rapid emergence of antimicrobial resistance (AMR) among bacterial pathogens results in antimicrobial treatment failure and the high mortality rate associated with AMR. The application of nanoparticles synthesized from probiotics will be widely accepted due to their efficacy and biocompatibility in treating microbial infections in humans. The current work sought to isolate and identify lactic acid bacteria (LAB) from Kimchi. Based on 16S rRNA gene sequencing, the LAB isolate C2 was identified as a member of the genus Leuconostoc. The obtained supernatant from Leuconostoc sp. strain C2 was employed for the green synthesis of metal (AuNPs) and metal oxide (ZnONPs) nanoparticles. UV–vis absorption spectra, FTIR analysis, XRD, DLS, FE-TEM, and EDS mapping were used to fully characterize these C2-AuNPs and C2-ZnONPs. The C2-AuNPs were found to be spherical in shape, with a size of 47.77 ± 5.7 nm and zeta potential of −19.35 ± 0.67 mV. The C2-ZnONPs were observed to be rod-shaped and 173.77 ± 14.53 nm in size. The C2-ZnONPs zeta potential was determined to be 26.62 ± 0.35 mV. The C2-AuNPs and C2-ZnONPs were shown to have antimicrobial activity against different pathogens. Furthermore, these nanoparticles inhibited the growth of Candida albicans. The antibiofilm and antivirulence properties of these NPs against Pseudomonas aeruginosa and Staphylococcus aureus were thoroughly investigated. C2-AuNPs were reported to be antibiofilm and antivirulence against P. aeruginosa, whereas C2-ZnONPs were antibiofilm and antivirulence against both P. aeruginosa and S. aureus. Furthermore, these nanoparticles disrupted the preformed mature biofilm of P. aeruginosa and S. aureus. The inhibitory impact was discovered to be concentration-dependent. The current research demonstrated that C2-AuNPs and C2-ZnONPs exhibited potential inhibitory effects on the biofilm and virulence features of bacterial pathogens. Further studies are needed to unravel the molecular mechanism behind biofilm inhibition and virulence attenuation.

Feed Safety and the Development of Poultry Intestinal Microbiota

Simple Summary

Intensive gut colonisation of animals starts immediately after birth or hatch. Oral route of colonisation, and consequently the first feed, plays a significant role in the continual defining of the intestinal microbial community. The feed can influence colonisation in two ways: providing the microbial inoculum and providing the nutritional requirements that suit a specific type of microbes. In combination with environmental factors, feed shapes animal’s future health and performance from the first day of life. The objective of this review was to investigate feed safety aspects of animal nutrition from the gut colonisation aspect.

Abstract

The first feed offered to young chicks is likely the most important meal in their life. The complex gut colonisation process is determined with early exposure and during the first days of life before the microbial community is formed. Therefore, providing access to high-quality feed and an environment enriched in the beneficial and deprived of pathogenic microorganisms during this period is critical. Feed often carries a complex microbial community that can contain major poultry pathogens and a range of chemical contaminants such as heavy metals, mycotoxins, pesticides and herbicides, which, although present in minute amounts, can have a profound effect on the development of the microbial community and have a permanent effect on bird’s overall health and performance. The magnitude of their interference with gut colonisation in livestock is yet to be determined. Here, we present the animal feed quality issues that can significantly influence the microbial community development, thus severely affecting the bird’s health and performance.

Application of a maximal-clique based community detection algorithm to gut microbiome data reveals driver microbes during influenza A virus infection

Influenza A Virus (IAV) infection followed by bacterial pneumonia often leads to hospitalization and death in individuals from high risk groups. Following infection, IAV triggers the process of viral RNA replication which in turn disrupts healthy gut microbial community, while the gut microbiota plays an instrumental role in protecting the host by evolving colonization resistance. Although the underlying mechanisms of IAV infection have been unraveled, the underlying complex mechanisms evolved by gut microbiota in order to induce host immune response following IAV infection remain evasive. In this work, we developed a novel Maximal-Clique based Community Detection algorithm for Weighted undirected Networks (MCCD-WN) and compared its performance with other existing algorithms using three sets of benchmark networks. Moreover, we applied our algorithm to gut microbiome data derived from fecal samples of both healthy and IAV-infected pigs over a sequence of time-points. The results we obtained from the real-life IAV dataset unveil the role of the microbial families Ruminococcaceae, Lachnospiraceae, Spirochaetaceae and Prevotellaceae in the gut microbiome of the IAV-infected cohort. Furthermore, the additional integration of metaproteomic data enabled not only the identification of microbial biomarkers, but also the elucidation of their functional roles in protecting the host following IAV infection. Our network analysis reveals a fast recovery of the infected cohort after the second IAV infection and provides insights into crucial roles of Desulfovibrionaceae and Lactobacillaceae families in combating Influenza A Virus infection. Source code of the community detection algorithm can be downloaded from https://github.com/AniBhar84/MCCD-WN.

Klebsiella pneumoniae l-Fucose Metabolism Promotes Gastrointestinal Colonization and Modulates Its Virulence Determinants

Colonization of the gastrointestinal (GI) tract by Klebsiella pneumoniae is generally considered asymptomatic. However, gut colonization allows K. pneumoniae to either translocate to sterile site within the same host or transmit through the fecal-oral route to another host. K. pneumoniae gut colonization is poorly understood, but knowledge of this first step toward infection and spread is critical for combatting its disease manifestations. K. pneumoniae must overcome colonization resistance (CR) provided by the host microbiota to establish itself within the gut. One such mechanism of CR is through nutrient competition. Pathogens that metabolize a broad range of substrates have the ability to bypass nutrient competition and overcome CR. Herein, we demonstrate that in response to mucin-derived fucose, the conserved fucose metabolism operon (fuc) of K. pneumoniae is upregulated in the murine gut, and we subsequently show that fucose metabolism promotes robust gut colonization. Growth studies using cecal filtrate as a proxy for the gut lumen illustrate the growth advantage that the fuc operon provides K. pneumoniae. We further show that fucose metabolism allows K. pneumoniae to be competitive with a commensal Escherichia coli isolate (Nissle). However, Nissle is eventually able to outcompete K. pneumoniae, suggesting that it can be utilized to enhance CR. Finally, we observed that fucose metabolism positively modulates hypermucoviscosity, autoaggregation, and biofilm formation but not capsule biogenesis. Together, these insights enhance our understanding of the role of alternative carbon sources in K. pneumoniae gut colonization and the complex relationship between metabolism and virulence in this species.

Prevalence of Bacterial Coinfections with Vibrio harveyi in the Industrialized Flow-through Aquaculture Systems in Hainan Province: A Neglected High-Risk Lethal Causative Agent to Hybrid Grouper

Vibrio harveyi is one of the most serious bacterial pathogens to aquatic animals worldwide. Evidence is mounting that coinfections caused by multiple pathogens are common in nature and can alter the severity of diseases in marine animals. However, bacterial coinfections involving V. harveyi have received little attention in mariculture. In this study, the results of pathogen isolation indicated that bacterial coinfection was a common and overlooked risk for hybrid groupers (♀ Epinephelus polyphekadion × ♂ E. fuscoguttatus) reared in an industrialized flow-through pattern in Hainan Province. The artificial infection in hybrid groupers revealed that coinfections with V. harveyi strain GDH11385 (a serious lethal causative agent to groupers) and other isolated pathogens resulted in higher mortality (46.67%) than infection with strain GDH11385 alone (33.33%), whereas no mortality was observed in single infection with other pathogens. Furthermore, the intestine, liver and spleen of hybrid groupers are target organs for bacterial coinfections involving V. harveyi. Based on the infection patterns found in this study, we propose that V. harveyi may have a specific spatiotemporal expression pattern of virulence genes when infecting the host. Taken together, bacterial coinfection with V. harveyi is a neglected high-risk lethal causative agent to hybrid groupers in the industrialized flow-through aquaculture systems in Hainan Province.

Interactions between Candida albicans and the resident microbiota

Candida albicans is a prevalent, opportunistic human fungal pathogen. It usually dwells in the human body as a commensal, however, once in its pathogenic state, it causes diseases ranging from debilitating superficial to life-threatening systemic infections. The switch from harmless colonizer to virulent pathogen is, in most cases, due to perturbation of the fungus-host-microbiota interplay. In this review, we focused on the interactions between C. albicans and the host microbiota in the mouth, gut, blood, and vagina. We also highlighted important future research directions. We expect that the evaluation of these interplays will help better our understanding of the etiology of fungal infections and shed new light on the therapeutic approaches.

Macrophages in the gut: Masters in multitasking

The gastrointestinal tract has the important task of absorbing nutrients, a complex process that requires an intact barrier allowing the passage of nutrients but that simultaneously protects the host against invading microorganisms. To maintain and regulate intestinal homeostasis, the gut is equipped with one of the largest populations of macrophages in the body. Here, we will discuss our current understanding of intestinal macrophage heterogeneity and describe their main functions in the different anatomical niches of the gut during steady state. In addition, their role in inflammatory conditions such as infection, inflammatory bowel disease, and postoperative ileus are discussed, highlighting the roles of macrophages in immune defense. To conclude, we describe the interaction between macrophages and the enteric nervous system during development and adulthood and highlight their contribution to neurodegeneration in the context of aging and diabetes.

Interactions between the gut microbiota-derived functional factors and intestinal epithelial cells - implication in the microbiota-host mutualism

Mutual interactions between the gut microbiota and the host play essential roles in maintaining human health and providing a nutrient-rich environment for the gut microbial community. Intestinal epithelial cells (IECs) provide the frontline responses to the gut microbiota for maintaining intestinal homeostasis. Emerging evidence points to commensal bacterium-derived components as functional factors for the action of commensal bacteria, including protecting intestinal integrity and mitigating susceptibility of intestinal inflammation. Furthermore, IECs have been found to communicate with the gut commensal bacteria to shape the composition and function of the microbial community. This review will discuss the current understanding of the beneficial effects of functional factors secreted by commensal bacteria on IECs, with focus on soluble proteins, metabolites, and surface layer components, and highlight the impact of IECs on the commensal microbial profile. This knowledge provides a proof-of-concept model for understanding of mechanisms underlying the microbiota-host mutualism.

Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense

Due to decreased immunity, both antibiotics and antifungals are regularly used in pediatric hematologic-cancer patients as a means to prevent severe infections and febrile neutropenia. The general effect of antibiotics on the human gut microbiome is profound, yielding decreased diversity and changes in community structure. However, the specific effect on pediatric oncology patients is not well-studied. The effect of antifungal use is even less understood, having been studied only in mouse models. Because the composition of the gut microbiome is associated with regulation of hematopoiesis, immune function and gastrointestinal integrity, changes within the patient gut can have implications for the clinical management of hematologic malignancies. The pediatric population is particularly challenging because the composition of the microbiome is age dependent, with some of the most pronounced changes occurring in the first three years of life. We investigated how antibiotic and antifungal use shapes the taxonomic composition of the stool microbiome in pediatric patients with leukemia and lymphoma, as inferred from both 16S rRNA and metagenome data. Associations with age, antibiotic use and antifungal use were investigated using multiple analysis methods. In addition, multivariable differential abundance was used to identify and assess specific taxa that were associated with multiple variables. Both antibiotics and antifungals were linked to a general decline in diversity in stool samples, which included a decrease in relative abundance in butyrate producers that play a critical role in host gut physiology (e.g., Faecalibacterium, Anaerostipes, Dorea, Blautia),. Furthermore, antifungal use was associated with a significant increase in relative abundance of opportunistic pathogens. Collectively, these findings have important implications for the treatment of leukemia and lymphoma patients. Butyrate is important for gastrointestinal integrity; it inhibits inflammation, reinforces colonic defense, mucosal immunity. and decreases oxidative stress. The routine use of broad-spectrum anti-infectives in pediatric oncology patients could simultaneously contribute to a decline in gastrointestinal integrity and colonic defense while promoting increases in opportunistic pathogens within the patient gut. Because the gut microbiome has been linked to both short-term clinical outcomes, and longer-lasting health effects, systematic characterization of the gut microbiome in pediatric patients during, and beyond, treatment is warranted.

Untangling the oral-gut axis in the pathogenesis of intestinal inflammation

An increasing body of literature reveals that host-microbe networks are well-coordinated and impact human health and disease. Recently, it has become evident that an abnormal alteration in bacterial configuration in the oral cavity, namely oral dysbiosis, caused by periodontal inflammation, is associated with various distant inflammatory diseases, including inflammatory bowel disease. However, the extent to which the relationships between oral and distant disorders are merely an association or are causally triggered by oral microorganisms remains debated. In this mini-review, we highlight mechanisms in inter-related organ system diseases , particularly the one between oral and gut inflammation. Further, we discuss clinical perspectives and propose a novel concept of a multi-hit hypothesis in the pathogenesis of gut inflammation, based on our updated knowledge of shared microbiological and immunological pathways between the oral and gut mucosae.

Bioengineered Probiotics: Synthetic Biology Can Provide Live Cell Therapeutics for the Treatment of Foodborne Diseases

The rising prevalence of antibiotic resistant microbial pathogens presents an ominous health and economic challenge to modern society. The discovery and large-scale development of antibiotic drugs in previous decades was transformational, providing cheap, effective treatment for what would previously have been a lethal infection. As microbial strains resistant to many or even all antibiotic drug treatments have evolved, there is an urgent need for new drugs or antimicrobial treatments to control these pathogens. The ability to sequence and mine the genomes of an increasing number of microbial strains from previously unexplored environments has the potential to identify new natural product antibiotic biosynthesis pathways. This coupled with the power of synthetic biology to generate new production chassis, biosensors and “weaponized” live cell therapeutics may provide new means to combat the rapidly evolving threat of drug resistant microbial pathogens. This review focuses on the application of synthetic biology to construct probiotic strains that have been endowed with functionalities allowing them to identify, compete with and in some cases kill microbial pathogens as well as stimulate host immunity. Weaponized probiotics may have the greatest potential for use against pathogens that infect the gastrointestinal tract: Vibrio cholerae, Staphylococcus aureus, Clostridium perfringens and Clostridioides difficile. The potential benefits of engineered probiotics are highlighted along with the challenges that must still be met before these intriguing and exciting new therapeutic tools can be widely deployed.

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters

Species belonging to the bacterial phyla Bacteroidetes and Firmicutes represent over 90% of the gastrointestinal microbiota. Changes in the ratio of these two bacterial groups were found to have contrasting health effects, including obesity and inflammatory diseases. Despite the availability of many bacterial genomes, comparative genomic studies on the gene pools of these two bacterial groups concerning cytochrome P450 monooxygenases (P450s), ferredoxins, and secondary metabolite biosynthetic gene clusters (smBGCs) are not reported. This study is aimed to address this research gap. The study revealed the presence of diverse sets of P450s, ferredoxins, and smBGCs in their genomes. Bacteroidetes species have the highest number of P450 families, ferredoxin cluster-types, and smBGCs compared to Firmicutes species. Only four P450 families, three ferredoxin cluster types, and five smBGCs are commonly shared between these two bacterial groups. Considering the above facts, we propose that the contrasting effects of these two bacterial groups on the host are partly due to the distinct nature of secondary metabolites produced by these organisms. Thus, the cause of the contrasting health effects of these two bacterial groups lies in their gene pools.