Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

Lycopene attenuates D-galactose-induced memory and behavioral deficits by mediating microbiota-SCFAs-gut-brain axis balance in female CD-1 mice

Aging impairs cognitive function, whereas nutritional intervention can delay aging and age-related diseases. Lycopene (LYC), a naturally occurring carotenoid, posses multiple health-promoting properties, including neuroprotective function. Here, the effects of LYC on memory and behavioral deficits induced by D-galactose (D-gal) treatment and the relative contribution of LYC-derived gut microbiota in these process were investigated. Results demonstrated that LYC showed effective protection on D-gal induced cognitive deficit and neuronal damage. Moreover, LYC treatment has beneficial effects on gut barrier damage, microbiota dysbiosis and levels of SCFAs in D-gal-induced subacute aging mice. Next, fecal microbiota transplantation (FMT) experiment was performed and increased SCFAs were observed in mice received stools from D-gal+LYC group when compared with D-gal-FMT group. Thus, we added SCFAs treatment served as a control group in order to evaluated whether the alterations of gut-brain axis could be attributed to LYC-reshaped gut microbiota and SCFAs. Results showed that recipient mice received SCFAs and stools from D-gal+LYC group have similar beneficial effects in improving gut and brain function, demonstrated as: improved intestinal health via elevating antioxidant enzymes contents, increasing the expressions of tight junctions proteins and protecting gut barrier, enhanced mice working memory capacity via alleviating hippocampal neurons impairment, improving synaptic function and enhancing mitochondrial function in the intestinal pseudo-aseptic mice. In conclusion, our results demonstrated that LYC-derived microbiome played a pivotal role in the regulation of cognitive functions during aging and enhanced SCFAs formation might be an important signaling molecule connecting gut microbiome and brain.

Comparative effects of non-fermented and Lacticaseibacillus paracasei-fermented pomelo juice on gut microbiota composition and short-chain fatty acid production: An in vitro colonic model

Pomelo juice, especially from the Tubtim Siam cultivar, may offer prebiotic benefits by promoting beneficial gut bacteria. This study evaluated the impact of non-fermented and Lacticaseibacillus paracasei (L. paracasei)-fermented pomelo juice on gut microbiota using an in vitro colonic fermentation model. The L. paracasei-fermented juice significantly increased lactobacilli levels compared to the non-fermented juice, while both treatments similarly suppressed coliforms within 24 h. Microbiota analysis revealed increased richness and significant community shifts in both treatments. Moreover, the fermented juice demonstrated a greater decrease in the Firmicutes/Bacteroidetes ratio, indicating a greater impact on gut metabolism. Fermented juice promoted beneficial bacteria like L. paracasei, Bifidobacterium longum, and Faecalibacterium prauznitzii while inhibiting pathogens. These changes coincided with higher production of short-chain fatty acids (SCFAs), including acetic, propionic, and n-butyric acids. Therefore, fermenting pomelo juice with L. paracasei improves its ability to beneficially influence the gut microbiota, suggesting its potential for gut health enhancement.

Fecal microbiome alterations of mice following immunization with gold nanoparticle vaccines against enterohemorrhagic Escherichia coli

BACKGROUND

Enterohemorrhagic Escherichia coli (EHEC), a group of enteric pathogenic bacteria that is a major cause of human diarrheal disease, must interact with the diverse intestinal microbiome during colonization and subsequently overcome the environmental challenges to survive and cause disease. While this relationship, and how the microbiome modulates infection of EHEC, has been studied, it is less understood how the microbiome is impacted during treatment for an EHEC infection. One area that is notably lacking in knowledge is how vaccination can impact the intestinal microbiome composition, and therefore, influence vaccine efficacy. We previously developed vaccine formulations consisting of gold nanoparticles (AuNPs) conjugated to various EHEC antigens and tested them in mice models using both EHEC and its murine counterpart Citrobacter rodentium. The goal of this study was to evaluate the relationship between these EHEC vaccines and their effects on the gut microbiome.

RESULTS

We found that immunization with the vaccines or adjuvant-only control did not lead to major alterations in the composition of the fecal microbiome; however, there were measurable variations in individual mice within the same vaccine group housed in separate cages. Also, immunization with one vaccine (AuNP-EscC) prevented both a decrease in the diversity of the fecal microbiome and an increase in detectable C. rodentium following infection compared to control animals.

CONCLUSIONS

Overall, our small study argues in favor of evaluating the intestinal microbiome during vaccine development not just for EHEC, but for other enteric pathogens.

Gut Pathogen Colonization: A Risk Factor to Bloodstream Infections in Preterm Neonates Admitted in the Neonatal Intensive Care Unit - A Prospective Cohort Study

INTRODUCTION

Gut pathogen colonization, where pathogens disrupt the normal gut microbiota, has been implicated in the development of bloodstream infections (BSIs). This study investigates the association between gut pathogen colonization and BSI, hypothesizing that species causing BSI primarily originated from gut.

METHODS

A prospective cohort study was conducted in the neonatal intensive care unit (NICU) of tertiary care hospital in Karnataka, India, from January 2021 to September 2023. Inborn preterm infants were enrolled. The study population was divided into two groups: group A (neonates without sepsis) and group B (neonates with sepsis). Demographic details and blood culture results were collected. Stool samples were taken on day 4 and day 14 for group A, and on day 4 and the day of sepsis diagnosis for group B.

RESULTS

Group B had a lower mean birthweight (1,649.6 ± 652.1 g) compared to group A (1,757 ± 656 g). Klebsiella pneumoniae was the most common pathogen causing BSIs (44.1%). The analysis revealed a high abundance of potential pathogens in the gut microbiome of group B neonates, with a concurrent decrease in beneficial gut flora.

CONCLUSION

This study provides strong evidence for the association between gut pathogen colonization and BSI development in preterm neonates in NICUs. Gut microbiota modulation may serve as preventive strategy against BSIs, emphasizing the need for further research in this area to improve outcomes in vulnerable population.

Nutrition of Escherichia coli within the intestinal microbiome

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

Perspectives on Microbiome Therapeutics in Infectious Diseases: A Comprehensive Approach Beyond Immunology and Microbiology

Although global life expectancy has increased over the past 20 years due to advancements in managing infectious diseases, one-fifth of people still die from infections. In response to this ongoing threat, significant efforts are underway to develop vaccines and antimicrobial agents. However, pathogens evolve resistance mechanisms, complicating their control. The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases. This highlights the urgent need for practical advancements, such as microbiome therapeutics, that address these limitations while complementing traditional approaches. Our review emphasizes key outcomes in the field, including evidence of probiotics reducing disease severity and insights into host-microbiome crosstalk that have informed novel therapeutic strategies. These findings underscore the potential of microbiome-based interventions to promote physiological function alongside existing strategies aimed at enhancing host immune responses and pathogen destruction. This narrative review explores microbiome therapeutics as next-generation treatments for infectious diseases, focusing on the application of probiotics and their role in host-microbiome interactions. While offering a novel perspective grounded in a cooperative defense system, this review also addresses the practical challenges and limitations in translating these advancements into clinical settings.

Invasive Fascioloides magna infections impact gut microbiota in a definitive host in Europe

Invasive parasites that expand their natural range can be a threat to wildlife biodiversity and may pose a health risk to non-adapted, naive host species. The invasive giant liver fluke, Fascioloides magna, native to North America, has extended its range in Europe and uses mainly red deer (Cervus elaphus) as definitive hosts. The penetration of the intestinal barrier by the young flukes to reach the liver via the abdominal cavity as well as the release of fluke metabolism products and excreta with the bile and/or changes in the microbial community of the biliary system may enable the translocation of intestinal bacteria across the intestinal barrier and, in turn, could be associated with inflammation and changes in the intestinal bacterial community. The gut commensal community plays a key role in host nutrition and interacts with cells of the immune system to maintain host health. For this study, the gut bacterial community of red deer infected with F. magna and of non-infected red deer from one of the largest forest ecosystems in Central Europe, located on the border between the Czech Republic and Germany, was investigated. The individual fluke burden was associated with changes in the gut microbial composition of the gut of infected individuals, whereas the diversity and composition of the gut bacteria were only slightly different between fluke-infected and uninfected deer. Several bacterial taxa at the genus level were unique to individuals carrying either one or many liver flukes. Our results suggest that the microbiota of red deer is stable to perturbation by low numbers of F. magna. However, a larger parasite burden may cause changes in the gut microbial composition in definitive hosts implying that non-invasive fecal microbiome assessments could serve as indicator for wildlife health monitoring.

Roles and occurrences of microbiota in the osmoregulatory organs, gills and gut, in marine medaka upon hypotonic stress

Gills and gut are the two primary osmoregulatory organs in fish. Recently, studies have expanded beyond the osmoregulatory mechanisms of these organs to explore the microbiota communities inhabiting them. It is now known that microbial communities in both organs shift in response to osmotic stress. However, there are limited studies identifying the major contributors and co-occurrence among these microbiota in both organs under seawater and freshwater transfer conditions. The current data mining report performed a bioinformatics analysis on two previous published datasets from our group, aiming to provide insights into host-bacteria relationships under osmotic stress. We divided the samples into four groups: control seawater gills (LSW); control seawater gut (TSW); freshwater transfer gills (LFW); and freshwater transfer gut (TFW). Our results showed that LSW had higher diversities, richness, and evenness compared to TSW. However, both the LFW and LSW did not show any significant differences after the freshwater transfer experiment. We further applied co-occurrence network analysis and, for the first time, reported on the interactions of taxa shaping the community structure in these two organs. Moreover, we identified enriched ectoine biosynthesis in seawater samples, suggesting its potential role in seawater environments. Increased mRNA expression levels of Na+/K+-atpase, and cftr, were observed in gills after 6 h of ectoine treatment. These findings provide a foundation for future studies on host-bacteria interactions under osmotic stress.

Fecal Microbiome Alterations of Mice Following Immunization with Gold Nanoparticle Vaccines Against Enterohemorrhagic Escherichia coli

Background

Enterohemorrhagic Escherichia coli (EHEC), a group of enteric pathogenic bacteria that is a major cause of human diarrheal disease, must interact with the diverse intestinal microbiome during colonization and subsequently overcome the environmental challenges to survive and cause disease. While this relationship, and how the microbiome modulates infection of EHEC, has been studied, it is less understood how the microbiome is impacted during treatment for an EHEC infection. One area that is notably lacking in knowledge is how vaccination can impact the intestinal microbiome composition, and therefore, influence vaccine efficacy. We previously developed vaccine formulations consisting of gold nanoparticles (AuNPs) conjugated to various EHEC antigens and tested them in small animal infection models using both EHEC and its murine counterpart Citrobacter rodentium. The goal of this study was to evaluate the relationship between these EHEC vaccines and their effects on the gut microbiome.

Results

We found that immunization with the vaccines or adjuvant-only control did not lead to major alterations in the composition of the fecal microbiome; however, there were measurable variations in individual mice within the same vaccine group housed in separate cages. Finally, immunization with one vaccine (AuNP-EscC) did prevent a decrease in the diversity of the fecal microbiome and an increase in detectable C. rodentium following infection compared to the control animals.

Conclusions

Overall, our small study argues in favor of evaluating the intestinal microbiome during vaccine development not just for EHEC, but for other enteric pathogens as well.

Microbiome and Hemato-immune Aging

The microbiome is a highly complex and diverse symbiotic component that undergoes dynamic changes with the organismal aging. Microbial perturbations, termed dysbiosis, exert strong influence on dysregulating the bone marrow niche and subsequently promoting the aging of hematopoietic and immune system. Accumulating studies have revealed the substantial impact of intestinal microbiome on the initiation and progression of age-related hematologic alteration and diseases, such as clonal hematopoiesis and blood cancers. Current therapeutic approaches to restore the altered microbiome diversity target specific pathobionts and are demonstrated to improve clinical outcomes of antihematologic malignancy treatments. In this review, we discuss the interplay between the microbiome and the hemato-immune system during aging process. We also shed light on the emerging therapeutic strategies to tackle the dysbiosis for amelioration of aging and disease progression.

Corynebacterial membrane vesicles disrupt cariogenic interkingdom assemblages

Polymicrobial diseases such as periodontal disease and caries pose significant treatment challenges due to their resistance to common approaches like antibiotic therapy. These infections exhibit increased resilience, due to microbial interactions that also disrupt host immune responses. Current research focuses on virulence and disease-promoting interactions, but less is known about interactions that could inhibit or prevent disease development. Normally human-associated microbiomes maintain homeostasis, preventing pathobionts from becoming dominant. In conditions like chronic disseminated candidiasis or severe early childhood caries (s-ECC), an overgrowth of microbes such as Candida albicans disrupts this balance. Typically, C. albicans coexists benignly within the microbial community but can become pathogenic, forming biofilms and interacting with other microbes such as cariogenic Streptococcus mutans. This interaction is particularly significant in s-ECC, where it exacerbates the disease's progression and severity. Here, we present that Corynebacterium durum, itself and through its extracellular membrane vesicles disrupts interkingdom assemblages between C. albicans and S. mutans. Mechanistically the interaction interference occurs at the genetic level with downregulated HWP1 expression, a surface protein specifically induced in the presence of S. mutans promoting the interkingdom interaction. Additionally, we show that C. durum can impede C. albicans systemic virulence in the Galleria mellonella infection model. This suggests that oral corynebacteria may act as a beneficial commensal species, exerting antifungal effects within polymicrobial communities and opening new avenues for managing polymicrobial diseases.IMPORTANCEPolymicrobial diseases such as severe early childhood caries (s-ECC) lack effective treatment options. Prevention, requiring a deeper understanding of ecological processes before the onset of disease symptoms, could be a potential strategy. In this context, we investigated how relatively abundant oral biofilm Corynebacterium species, which are associated with oral health, can interfere with the interkingdom partnership of Streptococcus mutans and Candida albicans. This partnership is a significant driver of tooth decay in s-ECC due to synergistic activities that increase cariogenicity. Our study reveals that oral corynebacteria, through the production of extracellular membrane vesicles, can disrupt the S. mutans and C. albicans partnership by inhibiting fungal hyphae formation. Additionally, the fatty acid cargo within these vesicles exhibits antifungal properties, suggesting that corynebacteria play a role in shaping microbial dynamics within the oral biofilm.

Alteration of the Gut-Lung Axis After Severe COVID-19 Infection and Modulation Through Probiotics: A Randomized, Controlled Pilot Study

BACKGROUND

The gut-lung axis could be a potential therapeutic target for improving post-acute COVID-19 symptoms, and probiotics have been proposed as possible modulators.

AIM

We conducted a pilot study to understand alterations in the gut-lung axis and to explore the effects of a probiotic in post-acute COVID-19 disease.

METHODS

We included patients after severe COVID-19 disease (sCOV, n = 21) in a randomized, placebo-controlled trial to test the effect of a probiotic (Pro-Vi 5, Institute Allergosan, Graz, Austria) in a six-month intervention and used patients after mild disease (mCOV, n = 10) as controls, to compare the intestinal microbiome, metabolome, and patient-reported outcomes and biomarkers along the gut-lung axis at baseline and throughout probiotic intervention.

RESULTS

Compared to mCOV patients, sCOV patients showed lower microbial richness, which was significantly improved by probiotic intervention. A reorganization of Ruminococcaceae and Lachnospiraceae taxa was observed in sCOV patients but remained unaffected by the intervention. Serum metabolome showed a dysregulation of lipoproteins in accordance with higher BMI and comorbidities in sCOV patients. HDL and LDL fractions/components were temporarily decreased in the probiotic group. Stool metabolome was altered at baseline in sCOV patients and an increase in L-DOPA after 3 months and butyrate after 6 months of intervention could be observed. Probiotics partially improved reduced quality of life and modulated altered immune responses in sCOV patients. Increased intestinal permeability at baseline remained unaffected.

CONCLUSION

The study provides evidence of long-term alterations of the gut-lung axis after severe COVID-19 infection and suggests that probiotics can modulate the biomarkers of the gut-lung axis.

Predisposition factors and control strategies of avian pathogenic Escherichia coli in laying hens

Shift in laying hens housing from conventional cage-based systems to alternatives has impacted their health and performance. Microorganisms colonize young chick in the early stages of their physiological and immune development. These colonizing microbes originate from parent and the environment. Escherichia coli is among the normal gut colonizing bacteria however, some E. coli strains known as avian pathogenic E. coli (APEC), cause local or systemic infections (colibacillosis) responsible of significant economic losses to the poultry industry. Potential APEC strains and other poultry gut microbiota are influenced by several factors such as housing system, and the use of feed additives (prebiotics, probiotics, symbiotic, among others). This review will discuss the status of pullets and layers immunity, gut health, and predisposing factors of colibacillosis. Dietary interventions and some colibacillosis mitigation strategies in pullets and laying hens are reviewed and discussed. With the development of sequencing technologies and the use of feed additives as alternatives to antibiotics, future studies need to understand some of the complex associations between the feed additives, the rearing environment, and their selective pressure on gut microbiota, including E. coli, and their impacts on immune development in pullets and hens.

Host-Pathogen Interactions during Shiga Toxin-Producing Escherichia coli Adherence and Colonization in the Bovine Gut: A Comprehensive Review

Shiga toxin-producing Escherichia coli (STEC) is a significant public health threat due to its ability to cause severe gastrointestinal diseases in humans, ranging from diarrhea to life-threatening conditions such as hemorrhagic colitis and hemolytic uremic syndrome (HUS). As the primary reservoir of STEC, cattle play a crucial role in its transmission through contaminated food and water, posing a considerable risk to human health. This comprehensive review explores host-pathogen interactions during STEC colonization of the bovine gut, focusing on the role of gut microbiota in modulating these interactions and influencing disease outcomes. We integrated findings from published transcriptomics, proteomics, and genomics studies to provide a thorough understanding of how STEC adheres to and colonizes the bovine gastrointestinal tract. The insights from this review offer potential avenues for the development of novel preventative and therapeutic strategies aimed at controlling STEC colonization in cattle, thereby reducing the risk of zoonotic transmission.

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities

The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.

Immune modulation and cecal microbiome changes in broilers fed with fenugreek seeds and Bacillus-based probiotics

Intensive broiler production systems face challenges like enteric diseases, impacting global food security. Strategies to enhance broiler immunity and gut health, particularly amidst antibiotic growth promoter restrictions, are crucial. The present study investigated the combined effects of fenugreek seeds (FS) and Bacillus-based direct-fed microbials (DFM) on immune-related gene expression in the ileum and alteration of microbial population in the cecum of broiler. The study involved 160 Ross 308 broiler chicks, which were divided into four groups consisting of 5 replicates, each containing eight birds. The chicks were grown for a period of 42 d, during which they had ad libitum access to feed and water. Dietary treatments were: Control (basal diet), FS5 (basal + 5g/kg fenugreek seeds), FS5DFM (basal + 5g/kg fenugreek seeds + 0.1g/kg Bacillus-based DFM), and DFM (basal + 0.1g/kg Bacillus-based DFM). Ileum tissue and cecal contents were collected on d 42 for gene expression and gut microbiome analysis. Ileal gene expression analysis revealed the downregulation of IL-6, IL-8L2, CASP6, PTGS2, and IRF7 in both FSs and DFMs groups compared to the control, suggesting individual immunomodulatory effects. However, avian β-defensin genes exhibited complex regulation, highlighting the need for further investigation. Cecal microbiome diversity remained stable, with subtle shifts in specific taxa influenced by FSs and DFMs. Interestingly, the combination of the FSs and DFMs uniquely impacted specific taxa, including Clostridiales vadin BB60. These findings suggest that both FSs and DFMs demonstrated potential for improving broiler immunity through inflammation reduction. The combination of FSs and DFMs offers a synergistic effect in immune modulation and specific microbial modulation, warranting further investigation with pathogen challenge models for comprehensive understanding.

Disruption of bacterial interactions and community assembly in Babesia-infected Haemaphysalis longicornis following antibiotic treatment

BACKGROUND

A previous study highlighted the role of antibiotic-induced dysbiosis in the tick microbiota, facilitating the transstadial transmission of Babesia microti from nymph to adult in Haemaphysalis longicornis. This study builds on previous findings by analyzing sequence data from an earlier study to investigate bacterial interactions that could be linked to enhanced transstadial transmission of Babesia in ticks. The study employed antibiotic-treated (AT) and control-treated (CT) Haemaphysalis longicornis ticks to investigate shifts in microbial community assembly. Network analysis techniques were utilized to assess bacterial interactions, comparing network centrality measures between AT and CT groups, alongside studying network robustness and connectivity loss. Additionally, functional profiling was conducted to evaluate metabolic diversity in response to antibiotic treatment.

RESULTS

The analysis revealed notable changes in microbial community assembly in response to antibiotic treatment. Antibiotic-treated (AT) ticks displayed a greater number of connected nodes but fewer correlations compared to control-treated (CT) ticks, indicating a less interactive yet more connected microbial community. Network centrality measures such as degree, betweenness, closeness, and eigenvector centrality, differed significantly between AT and CT groups, suggesting alterations in local network dynamics due to antibiotic intervention. Coxiella and Acinetobacter exhibited disrupted connectivity and roles, with the former showing reduced interactions in AT group and the latter displaying a loss of connected nodes, emphasizing their crucial roles in microbial network stability. Robustness tests against node removal showed decreased stability in AT networks, particularly under directed attacks, confirming a susceptibility of the microbial community to disturbances. Functional profile analysis further indicated a higher diversity and richness in metabolic capabilities in the AT group, reflecting potential shifts in microbial metabolism as a consequence of antimicrobial treatment.

CONCLUSIONS

Our findings support that bacterial interaction traits boosting the transstadial transmission of Babesia could be associated with reduced colonization resistance. The disrupted microbial interactions and decreased network robustness in AT ticks suggest critical vulnerabilities that could be targeted for managing tick-borne diseases.

Integrating functional metagenomics to decipher microbiome-immune interactions

Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.

Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case-control study in infectious diseases department

OBJECTIVE

Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage.

METHODS

We conducted a case-control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity.

RESULTS

Participants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27-44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini-Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β-diversity (Bray-Curtis dissimilarity index, p 0.42).

DISCUSSION

In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.

Exploring the Role of the Gut Microbiota in Modulating Colorectal Cancer Immunity

The gut microbiota plays an essential role in maintaining immune homeostasis and influencing the immune landscape within the tumor microenvironment. This review aims to elucidate the interactions between gut microbiota and tumor immune dynamics, with a focus on colorectal cancer (CRC). The review spans foundational concepts of immuno-microbial interplay, factors influencing microbiome composition, and evidence linking gut microbiota to cancer immunotherapy outcomes. Gut microbiota modulates anti-cancer immunity through several mechanisms, including enhancement of immune surveillance and modulation of inflammatory responses. Specific microbial species and their metabolic byproducts can significantly influence the efficacy of cancer immunotherapies. Furthermore, microbial diversity within the gut microbiota correlates with clinical outcomes in CRC, suggesting potential as a valuable biomarker for predicting response to immunotherapy. Conclusions: Understanding the relationship between gut microbiota and tumor immune responses offers potential for novel therapeutic strategies and biomarker development. The gut microbiota not only influences the natural history and treatment response of CRC but also serves as a critical modulator of immune homeostasis and anti-cancer activity. Further exploration into the microbiome's role could enhance the effectiveness of existing treatments and guide the development of new therapeutic modalities.

Impact of acute stress on the canine gut microbiota

There is growing evidence that a relationship exists between mental and emotional wellbeing and the gut microbiota. Little is known regarding how the microbiota reacts to repeated acute stress events in dogs, and whether it is a predictor of stress response. In this study, we explored the impact on the gut microbiota and digestive health with two common events many pet dogs find stressful. Twenty healthy adult dogs, living within a colony, were exposed to either car travel or separation three times across eight-week intervals. Faecal samples were collected 24 h before, within 24 h, and 24-48 h after. Faecal quality and pH, and microbiota diversity and composition were analysed in context with wider published work on physiological stress measures. No significant changes were observed in faecal quality or pH with either stress event at any timepoint, indicating all pets remained in good digestive health. Microbiota analysis demonstrated no significant impact on alpha or beta diversity with either stressor. Microbial signatures previously linked to stress were not identified in these dogs and no changes were observed in the functional gut composition. Irrespective of whether the pet was considered "stressed" (i.e., exhibited an increase in serum cortisol), there was no effect on the microbiota and no taxa were predictive of stress response. Collectively, this work demonstrates, for this population, certain acute stress events have no meaningful impact on the canine gut microbiota, and it has no impact on the associated stress response.

The microbiota: a crucial mediator in gut homeostasis and colonization resistance

The gut microbiota is a complex and diverse community of microorganisms that colonizes the human gastrointestinal tract and influences various aspects of human health. These microbes are closely related to enteric infections. As a foreign entity for the host, commensal microbiota is restricted and regulated by the barrier and immune system in the gut and contributes to gut homeostasis. Commensals also effectively resist the colonization of pathogens and the overgrowth of indigenous pathobionts by utilizing a variety of mechanisms, while pathogens have developed strategies to subvert colonization resistance. Dysbiosis of the microbial community can lead to enteric infections. The microbiota acts as a pivotal mediator in establishing a harmonious mutualistic symbiosis with the host and shielding the host against pathogens. This review aims to provide a comprehensive overview of the mechanisms underlying host-microbiome and microbiome-pathogen interactions, highlighting the multi-faceted roles of the gut microbiota in preventing enteric infections. We also discuss the applications of manipulating the microbiota to treat infectious diseases in the gut.

Unveiling the influence of a probiotic combination of Heyndrickxia coagulans and Lacticaseibacillus casei on healthy human gut microbiota using the TripleSHIME® system

Probiotics are host-friendly microorganisms that can have important health benefits in the human gut microbiota as dietary supplements. Maintaining a healthy gut microbial balance relies on the intricate interplay among the intestinal microbiota, metabolic activities, and the host's immune response. This study aims to explore if a mixture of Heyndrickxia coagulans [ATB-BCS-042] and Lacticaseibacillus casei [THT-030-401] promotes in vitro this balance in representative gut microbiota from healthy individuals using the Triple-SHIME® (Simulation of the Human Intestinal Microbial Ecosystem). Metataxonomic analysis of the intestinal microbes revealed that the probiotic mix was not causing important disruptions in the biodiversity or microbial composition of the three simulated microbiota. However, some targeted populations analyzed by qPCR were found to be disrupted at the end of the probiotic treatment or after one week of washout. Populations such as Cluster IV, Cluster XVIa, and Roseburia spp., were increased indicating a potential gut health-promoting butyrogenic effect of the probiotic supplementation. In two of the systems, bifidogenic effects were observed, while in the third, the treatment caused a decrease in bifidobacteria. For the health-detrimental biomarker Escherichia-Shigella, a mild decrease in all systems was observed in the proximal colon sections, but these genera were highly increased in the distal colon sections. By the end of the washout, Bacteroides-Prevotella was found consistently boosted, which could have inflammatory consequences in the intestinal context. Although the probiotics had minimal influence on most quantified metabolites, ammonia consistently decreased after one week of daily probiotic supplementation. In reporter gene assays, aryl hydrocarbon receptor (AhR) activation was favored by the metabolic output obtained from post-treatment periods. Exposure of a human intestinal cell model to fermentation supernatant obtained after probiotic supplementation induced a trend to decrease the mRNA expression of immunomodulatory cytokines (IL-6, IL-8). Overall, with some exceptions, a positive impact of H. coagulans and L. casei probiotic mix was observed in the three parallel experiments, despite inter-individual differences. This study might serve as an in vitro pipeline for the impact assessment of probiotic combinations on the human gut microbiota.

Interactions between Dietary Antioxidants, Dietary Fiber and the Gut Microbiome: Their Putative Role in Inflammation and Cancer

The intricate relationship between the gastrointestinal (GI) microbiome and the progression of chronic non-communicable diseases underscores the significance of developing strategies to modulate the GI microbiota for promoting human health. The administration of probiotics and prebiotics represents a good strategy that enhances the population of beneficial bacteria in the intestinal lumen post-consumption, which has a positive impact on human health. In addition, dietary fibers serve as a significant energy source for bacteria inhabiting the cecum and colon. Research articles and reviews sourced from various global databases were systematically analyzed using specific phrases and keywords to investigate these relationships. There is a clear association between dietary fiber intake and improved colon function, gut motility, and reduced colorectal cancer (CRC) risk. Moreover, the state of health is reflected in the reciprocal and bidirectional relationships among food, dietary antioxidants, inflammation, and body composition. They are known for their antioxidant properties and their ability to inhibit angiogenesis, metastasis, and cell proliferation. Additionally, they promote cell survival, modulate immune and inflammatory responses, and inactivate pro-carcinogens. These actions collectively contribute to their role in cancer prevention. In different investigations, antioxidant supplements containing vitamins have been shown to lower the risk of specific cancer types. In contrast, some evidence suggests that taking antioxidant supplements can increase the risk of developing cancer. Ultimately, collaborative efforts among immunologists, clinicians, nutritionists, and dietitians are imperative for designing well-structured nutritional trials to corroborate the clinical efficacy of dietary therapy in managing inflammation and preventing carcinogenesis. This review seeks to explore the interrelationships among dietary antioxidants, dietary fiber, and the gut microbiome, with a particular focus on their potential implications in inflammation and cancer.

A microfluidic co-culture model for investigating colonocytes-microbiota interactions in colorectal cancer

Changes in the abundance of certain bacterial species within the colorectal microbiota correlate with colorectal cancer (CRC) development. While carcinogenic mechanisms of single pathogenic bacteria have been characterized in vitro, limited tools are available to investigate interactions between pathogenic bacteria and both commensal microbiota and colonocytes in a physiologically relevant tumor microenvironment. To address this, we developed a microfluidic device that can be used to co-culture colonocyte spheroids and colorectal microbiota. The device was used to explore the effect of Fusobacterium nucleatum, an opportunistic pathogen associated with colorectal cancer development in humans, on colonocyte gene expression and microbiota composition. F. nucleatum altered the transcription of genes involved in cytokine production, epithelial-to-mesenchymal transition, and proliferation in colonocytes in a contact-independent manner; however, most of these effects were significantly diminished by the presence of commensal microbiota. Interestingly, F. nucleatum significantly altered the abundance of multiple bacterial clades associated with mucosal immune responses and cancer development in the colon. Our results highlight the importance of evaluating the potential carcinogenic activity of pathogens in the context of a commensal microbiota, and the potential to discover novel inter-species microbial interactions in the CRC microenvironment.

A Systematic Review on Antimicrobial Resistance in Ghana from a One Health Perspective

BACKGROUND

Antimicrobial resistance (AMR) poses a global health threat, with lower-middle-income countries bearing a disproportionate burden. Surveillance of AMR under a One Health framework is needed to elucidate the associations among clinical, animal, and environmental AMR. This review aimed to describe the state of AMR in Ghana, focusing on One Health.

METHOD

This review utilized the PRISMA guidelines and major databases to systematically search and analyze AMR in Ghana published from 1 January 2014 to 1 May 2023.

RESULTS

Out of the 48 articles that met the inclusion criteria, 28 studies were conducted on humans, 14 studies involved animals, and 6 studies focused on the environment. A total of 48 different pathogens were identified across the human, animal, and environmental sectors, with the most common being Escherichia coli (67%, n = 32), Klebsiella spp. (52%, n = 25), Pseudomonas spp. (40%, n = 19), and Salmonella spp. (38%, n = 18). Generally, a high prevalence of antibiotic resistance was observed among various bacterial species across the sectors. These bacteria exhibited resistance to commonly used antibiotics, with resistance to ampicillin and tetracycline exceeding 80%, and multidrug resistance (MDR) ranging from 17.6% in Shigella spp. to 100% in Acinetobacter spp.

CONCLUSION

This review reaffirms the significant challenge of AMR in Ghana, with a high prevalence observed in the human, animal, and environmental sectors. Key pathogens (e.g., Staphylococcus aureus and Escherichia coli) found across the sectors emphasize the urgent need for a One Health approach to tackle AMR in Ghana.

Moniezia benedeni infection increases IgE+ cells in sheep (Ovis aries) small intestine

The concentration of immunoglobulin (Ig) E is the lowest among serum Igs, but it can induces type I hypersensitivity and plays an important role in anti-parasitic infection. The present study aimed to explore the residence characteristics of IgE+ cells in the sheep small intestine and the impact of Moniezia benedeni infection on them. The recombinant plasmids pET-28a-IgE were constructed and induced and expressed in Escherichia coli. BL21 (DE3). The rabbit anti-sheep IgE polyclonal antibody was prepared using the obtained recombinant protein as antigen. Finally, the levels of IgE+ cells in the small intestine of healthy (Control group) and naturally M. benedeni-infected (Infected group) sheep were detected analyzed. The results showed that the rabbit anti-sheep IgE polyclonal antibody with good immunogenicity (titer = 1: 128000) could specifically bind to the heavy chain of natural sheep IgE. In the Control group, the IgE+ cells were mainly distributed in lamina propria of the small intestine, and the densities were significantly decreased from duodenum to ileum (P<0.05), with respective values of (4.28 cells / 104 μm2, 1.80 cells / 104 μm2, and 1.44 cells / 104 μm2 in duodenum, jejunum, and ileum. In the Infected group, IgE+ cells density were 6.26 cells / 104 μm2, 3.01 cells / 104 μm2, and 2.09 cells / 104 μm2 in duodenum, jejunum and ileum respectively, which were significantly higher in all segments compared to the Control group (P<0.05), increasing by 46.26%, 67.22% and 45.14%, respectively. In addition, compared with the Control group, the IgE protein levels were significantly increased in all intestinal segments of the Infected group (P<0.01), however, there was no significant differences among the different intestinal segments within the same group (P>0.05). The results demonstrated that M. benedeni infection could significantly increase the content of IgE and the distribution density of its secreting cells in sheep small intestine. The intestinal mucosal immune system of sheep presented obvious specificity against M. benedeni infection. This lays a good foundation for further exploring molecular mechanisms of the intestinal mucosal immune system monitoring and responding to M. benedeni infection.

Revolution in sepsis: a symptoms-based to a systems-based approach?

Severe infection and sepsis are medical emergencies. High morbidity and mortality are linked to CNS dysfunction, excessive inflammation, immune compromise, coagulopathy and multiple organ dysfunction. Males appear to have a higher risk of mortality than females. Currently, there are few or no effective drug therapies to protect the brain, maintain the blood brain barrier, resolve excessive inflammation and reduce secondary injury in other vital organs. We propose a major reason for lack of progress is a consequence of the treat-as-you-go, single-nodal target approach, rather than a more integrated, systems-based approach. A new revolution is required to better understand how the body responds to an infection, identify new markers to detect its progression and discover new system-acting drugs to treat it. In this review, we present a brief history of sepsis followed by its pathophysiology from a systems' perspective and future opportunities. We argue that targeting the body's early immune-driven CNS-response may improve patient outcomes. If the barrage of PAMPs and DAMPs can be reduced early, we propose the multiple CNS-organ circuits (or axes) will be preserved and secondary injury will be reduced. We have been developing a systems-based, small-volume, fluid therapy comprising adenosine, lidocaine and magnesium (ALM) to treat sepsis and endotoxemia. Our early studies indicate that ALM therapy shifts the CNS from sympathetic to parasympathetic dominance, maintains cardiovascular-endothelial glycocalyx coupling, reduces inflammation, corrects coagulopathy, and maintains tissue O2 supply. Future research will investigate the potential translation to humans.

A Review of the Mechanisms of Bacterial Colonization of the Mammal Gut

A healthy animal intestine hosts a diverse population of bacteria in a symbiotic relationship. These bacteria utilize nutrients in the host's intestinal environment for growth and reproduction. In return, they assist the host in digesting and metabolizing nutrients, fortifying the intestinal barrier, defending against potential pathogens, and maintaining gut health. Bacterial colonization is a crucial aspect of this interaction between bacteria and the intestine and involves the attachment of bacteria to intestinal mucus or epithelial cells through nonspecific or specific interactions. This process primarily relies on adhesins. The binding of bacterial adhesins to host receptors is a prerequisite for the long-term colonization of bacteria and serves as the foundation for the pathogenicity of pathogenic bacteria. Intervening in the adhesion and colonization of bacteria in animal intestines may offer an effective approach to treating gastrointestinal diseases and preventing pathogenic infections. Therefore, this paper reviews the situation and mechanisms of bacterial colonization, the colonization characteristics of various bacteria, and the factors influencing bacterial colonization. The aim of this study was to serve as a reference for further research on bacteria-gut interactions and improving animal gut health.

Ethanolamine metabolism through two genetically distinct loci enables Klebsiella pneumoniae to bypass nutritional competition in the gut

Successful microbial colonization of the gastrointestinal (GI) tract hinges on an organism's ability to overcome the intense competition for nutrients in the gut between the host and the resident gut microbiome. Enteric pathogens can exploit ethanolamine (EA) in the gut to bypass nutrient competition. However, Klebsiella pneumoniae (K. pneumoniae) is an asymptomatic gut colonizer and, unlike well-studied enteric pathogens, harbors two genetically distinct ethanolamine utilization (eut) loci. Our investigation uncovered unique roles for each eut locus depending on EA utilization as a carbon or nitrogen source. Murine gut colonization studies demonstrated the necessity of both eut loci in the presence of intact gut microbiota for robust GI colonization by K. pneumoniae. Additionally, while some Escherichia coli gut isolates could metabolize EA, other commensals were incapable, suggesting that EA metabolism likely provides K. pneumoniae a selective advantage in gut colonization. Molecular and bioinformatic analyses unveiled the conservation of two eut loci among K. pneumoniae and a subset of the related taxa in the K. pneumoniae species complex, with the NtrC-RpoN regulatory cascade playing a pivotal role in regulation. These findings identify EA metabolism as a critical driver of K. pneumoniae niche establishment in the gut and propose microbial metabolism as a potential therapeutic avenue to combat K. pneumoniae infections.

In vitro co-culture of Clostridium scindens with primary human colonic epithelium protects the epithelium against Staphylococcus aureus

A complex and dynamic network of interactions exists between human gastrointestinal epithelium and intestinal microbiota. Therefore, comprehending intestinal microbe-epithelial cell interactions is critical for the understanding and treatment of intestinal diseases. Primary human colonic epithelial cells derived from a healthy human donor were co-cultured with Clostridium scindens (C. scindens), a probiotic obligate anaerobe; Staphylococcus aureus (S. aureus), a facultative anaerobe and intestinal pathogen; or both bacterial species in tandem. The co-culture hanging basket platform used for these experiments possessed walls of controlled oxygen (O2) permeability to support the formation of an O2 gradient across the intestinal epithelium using cellular O2 consumption, resulting in an anaerobic luminal and aerobic basal compartment. Both the colonic epithelial cells and C. scindens remained viable over 48 h during co-culture. In contrast, co-culture with S. aureus elicited significant damage to colonic epithelial cells within 24 h. To explore the influence of the intestinal pathogen on the epithelium in the presence of the probiotic bacteria, colonic epithelial cells were inoculated sequentially with the two bacterial species. Under these conditions, C. scindens was capable of repressing the production of S. aureus enterotoxin. Surprisingly, although C. scindens converted cholic acid to secondary bile acids in the luminal medium, the growth of S. aureus was not significantly inhibited. Nevertheless, this combination of probiotic and pathogenic bacteria was found to benefit the survival of the colonic epithelial cells compared with co-culture of the epithelial cells with S. aureus alone. This platform thus provides an easy-to-use and low-cost tool to study the interaction between intestinal bacteria and colonic cells in vitro to better understand the interplay of intestinal microbiota with human colonic epithelium.

Microbial Metabolite Trimethylamine N-Oxide Promotes Campylobacter jejuni Infection by Escalating Intestinal Inflammation, Epithelial Damage, and Barrier Disruption

The interactions between Campylobacter jejuni , a critical foodborne cause of gastroenteritis, and the intestinal microbiota during infection are not completely understood. The crosstalk between C. jejuni and its host is impacted by the gut microbiota through mechanisms of competitive exclusion, microbial metabolites, or immune response. To investigate the role of gut microbiota on C. jejuni pathogenesis, we examined campylobacteriosis in the IL10KO mouse model, which was characterized by an increase in the relative abundance of intestinal proteobacteria, E. coli , and inflammatory cytokines during C. jejuni infection. We also found a significantly increased abundance of microbial metabolite Trimethylamine N-Oxide (TMAO) in the colonic lumens of IL10KO mice. We further investigated the effects of TMAO on C. jejuni pathogenesis. We determined that C. jejuni senses TMAO as a chemoattractant and the administration of TMAO promotes C. jejuni invasion into Caco-2 monolayers. TMAO also increased the transmigration of C. jejuni across polarized monolayers of Caco-2 cells, decreased TEER, and increased C. jejuni -mediated intestinal barrier damage. Interestingly, TMAO treatment and presence during C. jejuni infection of Caco-2 cells synergistically caused an increased inflammatory cytokine expression, specifically IL-1β and IL-8. These results establish that C. jejuni utilizes microbial metabolite TMAO for increased virulence during infection.

Overview of Bacterial Protein Toxins from Pathogenic Bacteria: Mode of Action and Insights into Evolution

Bacterial protein toxins are secreted by certain bacteria and are responsible for mild to severe diseases in humans and animals. They are among the most potent molecules known, which are active at very low concentrations. Bacterial protein toxins exhibit a wide diversity based on size, structure, and mode of action. Upon recognition of a cell surface receptor (protein, glycoprotein, and glycolipid), they are active either at the cell surface (signal transduction, membrane damage by pore formation, or hydrolysis of membrane compound(s)) or intracellularly. Various bacterial protein toxins have the ability to enter cells, most often using an endocytosis mechanism, and to deliver the effector domain into the cytosol, where it interacts with an intracellular target(s). According to the nature of the intracellular target(s) and type of modification, various cellular effects are induced (cell death, homeostasis modification, cytoskeleton alteration, blockade of exocytosis, etc.). The various modes of action of bacterial protein toxins are illustrated with representative examples. Insights in toxin evolution are discussed.

Clostridioides difficile recurrence in individuals with and without cancer: a Swedish population-based cohort study

PURPOSE

Patients with cancer are vulnerable to Clostridioides difficile infection (CDI) due to their disease, treatment and regular hospital contact, yet if CDI-recurrence is more common remains unclear, and differences among cancer types remain unexplored.

METHODS

This Swedish nationwide population-based cohort included all 43,150 individuals with recorded CDI (2006-2019) to assess CDI-recurrence in individuals with and without cancer, with binary multivariable logistic regression, stratified by anatomical location, and survival status.

RESULTS

Compared to those without cancer (N = 29,543), ongoing cancer (diagnosis < 12 months; N = 3,882) was associated with reduced recurrence (OR = 0.81, 95% CI 0.73-0.89), while there was no association with cancer history (diagnosis ≥ 12 months; N = 9,725). There was an increased 8-week all-cause mortality (Ongoing cancer: OR = 1.58, 95% CI 1.43-1.74; Cancer history: OR = 1.45, 95% CI 1.36-1.55) compared to those without cancer. Among CDI-survivors, those with ongoing cancer presented with a decreased odds of recurrence (OR = 0.84, 95% CI 0.76-0.94), compared to those without cancer history, with no association for those with cancer history (OR = 1.04, 95% CI 0.97-1.1). Large variations were seen across cancer types, with the highest observed proportion of recurrence in oral and mesothelial cancer, and the lowest for esophageal cancer, although no statistically significant OR were found.

CONCLUSION

The population-based study indicates that individuals with cancer may have fewerrecurrences than expected, yet variations by cancer type were large, and mortality was high.

Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution

Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.

Biomolecular Actions by Intestinal Endotoxemia in Metabolic Syndrome

Metabolic syndrome (MetS) is a combination of metabolic disorders that concurrently act as factors promoting systemic pathologies such as atherosclerosis or diabetes mellitus. It is now believed to encompass six main interacting conditions: visceral fat, imbalance of lipids (dyslipidemia), hypertension, insulin resistance (with or without impairing both glucose tolerance and fasting blood sugar), and inflammation. In the last 10 years, there has been a progressive interest through scientific research investigations conducted in the field of metabolomics, confirming a trend to evaluate the role of the metabolome, particularly the intestinal one. The intestinal microbiota (IM) is crucial due to the diversity of microorganisms and their abundance. Consequently, IM dysbiosis and its derivate toxic metabolites have been correlated with MetS. By intervening in these two factors (dysbiosis and consequently the metabolome), we can potentially prevent or slow down the clinical effects of the MetS process. This, in turn, may mitigate dysregulations of intestinal microbiota axes, such as the lung axis, thereby potentially alleviating the negative impact on respiratory pathology, such as the chronic obstructive pulmonary disease. However, the biomolecular mechanisms through which the IM influences the host's metabolism via a dysbiosis metabolome in both normal and pathological conditions are still unclear. In this study, we seek to provide a description of the knowledge to date of the IM and its metabolome and the factors that influence it. Furthermore, we analyze the interactions between the functions of the IM and the pathophysiology of major metabolic diseases via local and systemic metabolome's relate endotoxemia.

Effect of different forms of tobacco on the oral microbiome in healthy adults: a systematic review

Objective

The study aimed to evaluate the impact of tobacco use on the composition and functions of the oral microbiome in healthy adult humans.

Methods

We conducted a systematic search on PubMed, Web of Science, and Cinhal databases for literature published until 15 December 2023, to identify studies that have evaluated the oral microbiome with culture-independent next-generation techniques comparing the oral microbiome of tobacco users and non-users. The search followed the PECO format. The outcomes included changes in microbial diversity and abundance of microbial taxa. The quality assessment was performed using the Newcastle-Ottawa Scale (NOS) (PROSPERO ID CRD42022340151).

Results

Out of 2,435 articles screened, 36 articles satisfied the eligibility criteria and were selected for full-text review. Despite differences in design, quality, and population characteristics, most studies reported an increase in bacterial diversity and richness in tobacco users. The most notable bacterial taxa enriched in users were Fusobacteria and Actinobacteria at the phylum level and Streptococcus, Prevotella, and Veillonella at the genus level. At the functional level, more similarities could be noted; amino acid metabolism and xenobiotic biodegradation pathways were increased in tobacco users compared to non-users. Most of the studies were of good quality on the NOS scale.

Conclusion

Tobacco smoking influences oral microbial community harmony, and it shows a definitive shift towards a proinflammatory milieu. Heterogeneities were detected due to sampling and other methodological differences, emphasizing the need for greater quality research using standardized methods and reporting.

Systematic Review Registration

CRD42022340151.

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.

Type IV pilus retraction is required for Neisseria musculi colonization and persistence in a natural mouse model of infection

IMPORTANCE

We describe the importance of Type IV pilus retraction to colonization and persistence by a mouse commensal Neisseria, N. musculi, in its native host. Our findings have implications for the role of Tfp retraction in mediating interactions of human-adapted pathogenic and commensal Neisseria with their human host due to the relatedness of these species.

Current Approach to Complications and Difficulties during Transrectal Ultrasound-Guided Prostate Biopsies

Prostate cancer is one of the most common male malignancies worldwide. It affects middle-aged men (45-60 years) and is the leading cause of cancer-related mortality in Western countries. The TRUS (trans rectal ultrasound)-guided prostate biopsy has been a standard procedure in prostate cancer detection for more than thirty years, and it is recommended in male patients with an abnormal PSA (prostate-specific antigens) or abnormalities found during digital rectal examinations. During this procedure, urologists might encounter difficulties which may cause subsequent complications. This manuscript aims to present both the complications and the technical difficulties that may occur during TRUS-guided prostate biopsy, along with resolutions and solutions found in the specialized literature. The conclusions of this manuscript will note that the TRUS-guided prostate biopsy remains a solid, cost-efficient, and safe procedure with which to diagnose prostate cancer. The complications are usually self-limiting and do not require additional medical assistance. The difficulties posed by the procedure can be safely overcome if there are no other available alternatives. Open communication with the patients improves both pre- and post-procedure compliance.

Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes

Prior work has shown a positive scaling relationship between vertebrate body size, human height, and gut microbiome alpha diversity. This observation mirrors commonly observed species area relationships (SARs) in many other ecosystems. Here, we expand these observations to several large datasets, showing that this size-diversity scaling relationship is independent of relevant covariates, like diet, body mass index, age, sex, bowel movement frequency, antibiotic usage, and cardiometabolic health markers. Island biogeography theory (IBT), which predicts that larger islands tend to harbor greater species diversity through neutral demographic processes, provides a simple mechanism for positive SARs. Using a gut-adapted IBT model, we demonstrated that increasing the length of a flow-through ecosystem led to increased species diversity, closely matching our empirical observations. We delve into the possible clinical implications of these SARs in the American Gut cohort. Consistent with prior observations that lower alpha diversity is a risk factor for Clostridioides difficile infection (CDI), we found that individuals who reported a history of CDI were shorter than those who did not and that this relationship was mediated by alpha diversity. We observed that vegetable consumption had a much stronger association with CDI history, which was also partially mediated by alpha diversity. In summary, we find that the positive scaling observed between body size and gut alpha diversity can be plausibly explained by a gut-adapted IBT model, may be related to CDI risk, and vegetable intake appears to independently mitigate this risk, although additional work is needed to validate the potential disease risk implications.

The effects of starvation stress on intestinal morphology and flora of grass carp (Ctenopharyngodon idella)

Starvation stress can profoundly impact various physiological parameters in fish, including metabolism, behavior, meat quality, and reproduction. However, the repercussions of starvation on the intestinal microbiota of grass carp remain under-explored. This research aimed to elucidate the effects of a 28-day starvation period on the composition of the intestinal microbiota of grass carp. Tissue pathology assessments revealed significant alterations in the dimensions of intestinal villi in the foregut, midgut, and hindgut as compared to the controls. Specifically, dominant differences appeared in both the length and width of the villi. Moreover, a marked decline in the goblet cell population was observed across all the intestinal segments. 16S rDNA sequencing was used to investigate changes in the gut microbiota, which revealed distinct clustering patterns among the starved and control groups. While α diversity metrics remained consistent for the anterior intestine, significant deviations were recorded in the Shannon (midgut: ***P < 0.001; hindgut: *P < 0.05) and Simpson indices (midgut and hindgut: ***P < 0.001), demonstrating alterations in microbial richness and evenness. At the phylum level, Proteobacteria, Bacteroidetes, and Fusobacteria emerged as dominant groups post-starvation. Other bacterial taxa, such as Actinobacteria and Verrucomicrobia, decreased, whereas Bacteroidetes and Firmicutes showed a small increase. In summation, starvation induces considerable morphological and microbial shifts in the grass carp intestine, and thus, this study offers valuable insights into their cultivation strategies.

No fitness cost entailed by type VI secretion system synthesis, assembly, contraction, or disassembly in enteroaggregative Escherichia coli

IMPORTANCE

Bacteria use weapons to deliver effectors into target cells. One of these weapons, the type VI secretion system (T6SS), assembles a contractile tail acting as a spring to propel a toxin-loaded needle. Due to its size and mechanism of action, the T6SS was intuitively thought to be energetically costly. Here, using a combination of mutants and growth measurements in liquid medium, on plates, and in competition experiments, we show that the T6SS does not entail a growth cost to enteroaggregative Escherichia coli.

Microbiota Composition and Probiotics Supplementations on Sleep Quality-A Systematic Review and Meta-Analysis

The gut microbiota (GM) plays a crucial role in human health. The bidirectional interaction between GM and the central nervous system may occur via the microbiota-gut-brain axis, possibly regulating the sleep/wake cycle. Recent reports highlight associations between intestinal dysbiosis and sleep disorders, suggesting that probiotics could ameliorate this condition. However, data are poor and inconsistent. The aim of this quantitative metanalytic study is to assess the GM composition in sleep disturbances and evaluate probiotics' effectiveness for managing sleep disorders. A systematic review was carried out until July 2022 in online databases, limiting the literature research to human studies and English language articles. No significant GM diversity between patients with sleep disturbances versus healthy controls was found, revealed by α-diversity, while β-diversity is missing due to lack of proper reporting. However, probiotics supplementation significantly reduced the self-assessed parameter of sleep quality and disturbances Pittsburgh Sleep Quality Index (PSQI) score compared with the placebo. No difference in the Epworth Sleepiness Scale (ESS) score was found. While available data suggest that GM diversity is not related to sleep disturbances, probiotics administration strongly improves sleep quality as a subjective perception. However, heterogeneity of data reporting in the scientific literature should be considered as a limitation.

Dynamic Interactions between Diarrhoeagenic Enteroaggregative Escherichia coli and Presumptive Probiotic Bacteria: Implications for Gastrointestinal Health

This study delves into the temporal dynamics of bacterial interactions in the gastrointestinal tract, focusing on how probiotic strains and pathogenic bacteria influence each other and human health. This research explores adhesion, competitive exclusion, displacement, and inhibition of selected diarrhoeagenic Escherichia coli (D-EAEC) and potential probiotic strains under various conditions. Key findings reveal that adhesion is time-dependent, with both D-EAEC K2 and probiotic L. plantarum FS2 showing increased adhesion over time. Surprisingly, L. plantarum FS2 outperformed D-EAEC K2 in adhesion and exhibited competitive exclusion and displacement, with inhibition of adhesion surpassing competitive exclusion. This highlights probiotics' potential to slow pathogen attachment when not in competition. Pre-infecting with L. plantarum FS2 before pathogenic infection effectively inhibited adhesion, indicating probiotics' ability to prevent pathogen attachment. Additionally, adhesion correlated strongly with interleukin-8 (IL-8) secretion, linking it to the host's inflammatory response. Conversely, IL-8 secretion negatively correlated with trans-epithelial electrical resistance (TEER), suggesting a connection between tight junction disruption and increased inflammation. These insights offer valuable knowledge about the temporal dynamics of gut bacteria interactions and highlight probiotics' potential in competitive exclusion and inhibiting pathogenic bacteria, contributing to strategies for maintaining gastrointestinal health and preventing infections.

Impact of glyphosate (RoundupTM) on the composition and functionality of the gut microbiome

Glyphosate, the active ingredient in the broad-spectrum herbicide RoundupTM, has been a topic of discussion for decades due to contradictory reports of the effect of glyphosate on human health. Glyphosate inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) of the shikimic pathway producing aromatic amino acids in plants, a mechanism that suggests that the herbicide would not affect humans as this pathway is not found in mammals. However, numerous studies have implicated glyphosate exposure in the manifestation of a variety of disorders in the human body. This review specifically outlines the potential effect of glyphosate exposure on the composition and functionality of the gut microbiome. Evidence has been building behind the hypothesis that the composition of each individual gut microbiota significantly impacts health. For this reason, the potential of glyphosate to inhibit the growth of beneficial microbes in the gut or alter their functionality is an important topic that warrants further consideration.

Impact of intestinal colonization by Gram-negative bacteria on the incidence of bloodstream infections and lethality in critically ill neonates

BACKGROUND

Early detection of antimicrobial-resistant microorganisms is crucial to prevent subsequent invasive infections and contain their spread in the Neonatal Intensive Care Unit (NICU). This study aims to investigate the association between intestinal colonization (IC) by Gram-negative bacteria and the risk of bloodstream infection (BSI) in critically ill neonates.

METHODS

Data from the electronic medical records of 678 newborns admitted to a NICU Brazilian between 2018 and 2022 were retrospectively analyzed. Participants were monitored by the National Health Security Network.

RESULTS

Among neonates, 6.9 % had IC (56.9 % attributed to Acinetobacter baumannii); of these, 19.1 % developed BSI (66.7 % by Staphylococcus spp.). Within the A. baumannii colonization, 34.5 % occurred during an outbreak in September 2021. Colonized individuals had a longer mean length of stay (49.3 ± 26.4 days) and higher mortality rate (12.8 %) compared to non-colonized individuals (22.2 ± 16.9 days; 6.7 %, respectively). Previous use of antimicrobials and invasive devices significantly increased the risk of colonization. Colonization by drug-resistant microorganisms, along with the occurrence of BSI, was associated with increased mortality and reduced survival time.

CONCLUSIONS

IC contributed to the incidence of BSI, leading to more extended hospital stays and higher mortality rates. Its early detection proved to be essential to identify an outbreak and control the spread of resistant microorganisms within the NICU.

Identification of intestinal and fecal microbial biomarkers using a porcine social stress model

Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.

The oral-gut axis: a missing piece in the IBD puzzle

Inflammatory bowel disease (IBD) is a multifactorial intractable intestinal disease. Focusing on only one facet of the pathogenesis of IBD is insufficient to fully capture the complexity of the disease, and results in limited advance in clinical management. Therefore, it is critical to dissect the interactions amongst the multifarious contributors to the pathogenesis to comprehensively understand its pathology and subsequently improve clinical outcomes. In this context, the systemic interactions between organs, particularly the oral-gut axis mediated by host immune cells and resident microorganisms, have garnered significant attention in IBD research. More specifically, periodontal disease such as periodontitis has been implicated in augmenting intestinal inflammation beyond the confines of the oral cavity. There is mounting evidence suggesting that potentially harmful oral resident bacteria, termed pathobionts, and pro-inflammatory immune cells from the oral mucosa can migrate to the gastrointestinal tract, thereby potentiating intestinal inflammation. This article aims to provide a holistic overview of the causal relationship between periodontal disease and intestinal inflammation. Furthermore, we will discuss potential determinants that facilitate the translocation of oral pathobionts into the gut, a key event underpinning the oral-gut axis. Unraveling the complex dynamics of microbiota and immunity in the oral-gut continuum will lead to a better understanding of the pathophysiology inherent in both oral and intestinal diseases and the development of prospective therapeutic strategies.

Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community

IMPORTANCE

The development of probiotic therapies targeted at the small intestinal microbiota represents a significant advancement in the field of probiotic interventions. This region poses unique opportunities due to its low number of gut microbiota, along with the presence of heightened immune and metabolic host responses. However, progress in this area has been hindered by a lack of detailed understanding regarding the molecular mechanisms through which probiotics exert their effects in the small intestine. Our study, utilizing a synthetic community of three small intestinal bacterial strains and the addition of two different probiotic species, and kynurenine as a representative dietary or endogenously produced compound, highlights the importance of selecting probiotic species with diverse genetic capabilities that complement the functional capacity of the resident microbiota, or alternatively, constructing a multispecies formula. This approach holds great promise for the development of effective probiotic therapies and underscores the need to consider the functional capacity of probiotic species when designing interventions.