Butyrate specifically down-regulates salmonella pathogenicity island 1 gene expression

Exploring the Potential of Novel Animal-Origin Probiotics as Key Players in One Health: Opportunities and Challenges

Probiotics play a critical role in promoting the health of both humans and animals, with growing interest in the potential of animal-derived strains. Safety and efficacy assessments are crucial, with rigorous testing required to ensure the absence of harmful effects. The health benefits of animal-derived probiotic strains include improved digestion, balanced microbiota, behavioral impact, reduced inflammation, and minimized risk of infections. Probiotics of animal origin show promise as complementary or alternative options to antibiotics, with potential applications in both veterinary and human medicine. While promising, the usage of animal-derived probiotics requires careful evaluation of safety and regulatory aspects. This research underscores their potential for promoting health across species and contributing to future therapeutic approaches.

Evaluation of commercial diets on fecal consistency and defecation frequency in rhesus macaques (Macaca mulatta) with chronic intermittent idiopathic diarrhea

BACKGROUND

Recurrent diarrhea is common health and welfare problem in captive rhesus macaques (Macaca mulatta). Aside from infectious causes, dietary factors have been implicated in diarrhea. Therefore, the main objective of this study was to evaluate commercially available pelleted diets in rhesus macaques with chronic intermittent idiopathic diarrhea. The main differences between these diets were lactose and fiber content. A randomized cross-over diet study was conducted to investigate the influence of each diet on fecal consistency and defecation frequency as indicators of diarrhea. Nine animals with chronic intermittent diarrhea and four controls were included. Each diet was fed for approximately three months, with a similar wash-out period after each diet cycle. The fecal consistency was graded using the Waltham Faeces Scoring system, with a cutoff score of > 3.5 indicating diarrhea. Both groups and diets were compared by both mixed and fixed effect models.

RESULTS

Descriptive data showed that the mean fecal consistency score was highest in the diarrhea group in the standard diet at 3.71 ± 0.456 whereas the lowest mean fecal consistency scores were observed for lactose-free and high fiber diet in both diarrhea (3.25 ± 0.423) and control group (3.04 ± 0.346). A significant improvement of the fecal consistency score was detected in the diarrhea group when fed lactose-free diets (-0.41(-0.65 - -0.16, P < 0.01) and -0.47(-0.68 --0.25, P < 0.0002), respectively). Lactose-free and high fiber content showed the best outcome regarding improvement of the fecal consistency score -0.47(CL -0.68-- 0.25, P < 0.0002). Defecation frequency increased in both groups with 1.21(CL 0.65 - 1.78, P < 0.00001) per observation day when fed a lactose-free, high-fiber diet.

CONCLUSIONS

Lactose-free and high-fiber showed overall the best improvement of the fecal consistency in animals with diarrhea. Switching to commercially available lactose-free diets may decrease diarrhea incidence in rhesus macaques suffering from chronic intermittent idiopathic diarrhea. Nevertheless, additional nutritional research is warranted and establishing optimal nutritional requirements for captive macaques will add to our ability to understand and improve dietary interventions.

Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function

BACKGROUND

Promoting resistance to enteric pathogen infection is a core function of the gut microbiota; however, many of the specific host-commensal interactions that mediate this protection remain uncharacterised. To address this knowledge gap, we monocolonised germ-free mice with mouse-derived commensal microbes to screen for microbiota-induced resistance to Salmonella Typhimurium infection.

RESULTS

We identified Enterocloster clostridioformis as a protective species against S. Typhimurium infection. E. clostridioformis selectively upregulates resistin-like molecule β and cell cycle pathway expression at the level of caecal epithelial cells and increases T-regulatory cells in the underlying mucosal immune system, potentially contributing to reduced infection-induced pathology.

CONCLUSIONS

We highlight novel mechanisms of host-microbe interactions that can mediate microbiota-induced resistance to acute salmonellosis. In the backdrop of increasing antibiotic resistance, this study identifies novel potential avenues for further research into protective host responses against enteric infections and could lead to new therapeutic approaches. Video Abstract.

Phage-resistance alters Lipid A reactogenicity: a new strategy for LPS-based conjugate vaccines against Salmonella Rissen

Salmonella enterica serovar Rissen (S. Rissen) is an emerging causative agent of foodborne diseases. The current emergence of antibiotic resistance makes necessary alternative therapeutic strategies. In this study, we investigated the potential of a phage-resistant strain of S. Rissen (RR) as a tool for developing an effective lipopolysaccharide (LPS)-based vaccine. The LPS O-antigen is known to play critical roles in protective immunity against Salmonella. However, the high toxicity of the LPS lipid A moiety limits its use in vaccines. Here, we demonstrated that the acquisition of bacteriophage resistance by S. Rissen leads to structural modifications in the LPS structure. Using NMR and mass spectrometry, we characterized the LPS from phage-resistant strains as a smooth variant bearing under-acylated Lipid A portions (penta- and tetra-acylated forms). We then combined RT-qPCR and NMR-based metabolomics to explore the effects of phage resistance and LPS modification on bacterial fitness and virulence. Finally, we conducted in vivo studies to determine whether lysogeny-induced remodeling of LPS affects the host immune response. Results revealed that the under-acylated variant of LPS from RR attenuates the inflammatory response in BALB/c mice, while eliciting a specific antibody response that protects against S. Rissen (RW) infection. In conclusion, our findings suggest that phage resistance, through lipid A modification, may offer a novel strategy for reducing LPS toxicity, highlighting its potential as a promising biological approach for developing LPS-based vaccines against Salmonella infections.

Gut microbiota-derived butyrate improved acute leptospirosis in hamster via promoting macrophage ROS mediated by HDAC3 inhibition

Leptospirosis is a re-emerging worldwide zoonotic disease. Infected patients and animals often exhibit intestinal symptoms. Mounting evidence suggests that host immune responses to bacterial infection are closely associated with intestinal homeostasis. Our previous research has shown that the gut microbiota can protect the host from acute leptospirosis, while the specific bacterial metabolic mediators participating in the pathogenesis remain to be identified. Short-chain fatty acids (SCFAs) are metabolites produced mainly by the gut microbiota that play a role in immune regulation. However, whether SCFAs are the key to protecting the host against leptospirosis and the underlying regulatory mechanisms are unknown. In this study, our results showed that the SCFA butyrate is involved in ameliorating leptospirosis. The depletion of SCFAs by antibiotic cocktail treatment reduced survival time after Leptospira infection while supplementation with butyrate but not acetate or propionate significantly amelioration of leptospirosis. In vitro experiments showed that butyrate treatment enhanced the intracellular bactericidal activity mediated by reactive oxygen species (ROS) production. Mechanistically, butyrate functions as a histone deacetylase 3 inhibitor (HDAC3i) to promote ROS production via monocarboxylate transporter (MCT). The protection of butyrate against acute leptospirosis mediated by ROS was also proven in vivo. Collectively, our data provide evidence that the butyrate-MCT-HDAC3i-ROS signaling axis is a potential therapeutic target for acute leptospirosis. Our work not only interprets the microbial metabolite signaling involved in transkingdom interactions between the host and gut microbiota but also provides a possible target for developing a prevention strategy for acute leptospirosis.

IMPORTANCE

Leptospirosis is a worldwide zoonotic disease caused by Leptospira. An estimated 1 million people are infected with leptospirosis each year. Studies have shown that healthy gut microbiota can protect the host against leptospirosis but the mechanism is not clear. This work elucidated the mechanism of gut microbiota protecting the host against acute leptospirosis. Here, we find that butyrate, a metabolite of gut microbiota, can improve the survival rate of hamsters with leptospirosis by promoting the bactericidal activity of macrophages. Mechanistically, butyrate upregulates reactive oxygen species (ROS) levels after macrophage infection with Leptospira by inhibiting HDAC3. This work confirms the therapeutic potential of butyrate in preventing acute leptospirosis and provides evidence for the benefits of the macrophage-HDAC3i-ROS axis.

Lactiplantibacillus argentoratensis AGMB00912 alleviates diarrhea and promotes the growth performance of piglets during the weaning transition

BACKGROUND

Preventing post-weaning diarrhea (PWD) in weaned piglets is a crucial challenge in the swine production industry. The stress of weaning, dietary shifts from maternal milk to solid feed, and environmental changes lead to decreased microbial diversity, increased pathogen abundance, and compromised intestinal integrity. We have previously identified Lactiplantibacillus argentoratensis AGMB00912 (LA) in healthy porcine feces, which demonstrated antimicrobial activity against pathogens and enhanced short-chain fatty acid production. This research aimed to evaluate the efficacy of LA strain supplementation as a strategy to inhibit PWD and enhance overall growth performance in weaned piglets.

RESULTS

LA supplementation in weaned piglets significantly increased body weight gain, average daily gain, and average daily feed intake. It also alleviated diarrhea symptoms (diarrhea score and incidence). Notably, LA was found to enrich beneficial microbial populations (Lactobacillus, Anaerobutyricum, Roseburia, Lachnospiraceae, and Blautia) while reducing the abundance of harmful bacteria (Helicobacter and Campylobacter). This not only reduces the direct impact of pathogens but also improves the overall gut microbiota structure, thus enhancing the resilience of weaned piglets. LA treatment also promotes the growth of the small intestinal epithelial structure, strengthens gut barrier integrity, and increases short-chain fatty acid levels in the gut.

CONCLUSIONS

The study findings demonstrate the promising potential of LA in preventing PWD. Supplementation with the LA strain offers a promising feed additive for improving intestinal health and growth in piglets during the weaning transition, with the potential to significantly reduce the incidence and severity of PWD.

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.

It Is All about Probiotics to Control Cervical Cancer

Cervical cancer (CC) is the fourth most common malignancy in female patients. "Human papillomavirus" (HPV) contamination is a leading cause of all forms of cervical cancer, accounting for an expected 570,000 reported incidents in 2018. Two HPV strains (16 and 18) are responsible for 70% of CC and pre-cancerous cervical abnormalities. CC is one of the foremost reasons for the malignancy death rate in India among women ranging from 30 to 69 years of age in India, responsible for 17% of all cancer deaths. Currently approved cervical cancer treatments are associated with adverse reactions that might harm the lives of women affected by this disease. Consequently, probiotics can play a vital role in the treatment of CC. It is reflected from various studies regarding the role of probiotics in the diagnosis, prevention or treatment of cancer. In this review article, we have discussed the rationale of probiotics for treatment of CC, the role of probiotics as effective adjuvants in anti-cancer therapy and the combined effect of the anti-cancer drug along with probiotics to minimize the side effects due to chemotherapy.

Antibiotic-induced microbiome depletion promotes intestinal colonization by Campylobacter jejuni in mice

BACKGROUND

To establish a method to induce Campylobacter jejuni colonization in the intestines of C57BL/6 mice through antibiotic-induced microbiome depletion.

RESULTS

Fifty-four female C57BL/6 mice were divided into the normal, control, and experimental groups. The experimental group was administered intragastric cefoperazone sodium and sulbactam sodium (50 mg/mL) for 2 days; then, the experimental and control mice were intragastrically administered 200 µL C. jejuni, which was repeated once more after 2 days. Animal feces were collected, and the HipO gene of C. jejuni was detected using TaqMan qPCR from day 1 to day 14 after modeling completion. Immunofluorescence was used to detect intestinal C. jejuni colonization on day 14, and pathological changes were observed using hematoxylin and eosin staining. Additionally, 16S rDNA analyses of the intestinal contents were conducted on day 14. In the experimental group, C. jejuni was detected in the feces from days 1 to 14 on TaqMan qPCR, and immunofluorescence-labeled C. jejuni were visibly discernable in the intestinal lumen. The intestinal mucosa was generally intact and showed no significant inflammatory-cell infiltration. Diversity analysis of the colonic microbiota showed significant inter-group differences. In the experimental group, the composition of the colonic microbiota differed from that in the other 2 groups at the phylum level, and was characterized by a higher proportion of Bacteroidetes and a lower proportion of Firmicutes.

CONCLUSIONS

Microbiome depletion induced by cefoperazone sodium and sulbactam sodium could promote long-term colonization of C. jejuni in the intestines of mice.

Friend or Foe: Exploring the Relationship between the Gut Microbiota and the Pathogenesis and Treatment of Digestive Cancers

Digestive cancers are among the leading causes of cancer death in the world. However, the mechanisms of cancer development and progression are not fully understood. Accumulating evidence in recent years pointing to the bidirectional interactions between gut dysbiosis and the development of a specific type of gastrointestinal cancer is shedding light on the importance of this "unseen organ"-the microbiota. This review focuses on the local role of the gut microbiota imbalance in different digestive tract organs and annexes related to the carcinogenic mechanisms. Microbiota modulation, either by probiotic administration or by dietary changes, plays an important role in the future therapies of various digestive cancers.

Differences in bacterial taxa between treatment-naive patients with major depressive disorder and non-affected controls may be related to a proinflammatory profile

BACKGROUND

Major depressive disorder (MDD) is characterized by sadness and anhedonia, but also physical symptoms such as changes in appetite and weight. Gut microbiota has been hypothesized to be involved in MDD through gut-brain axis signaling. Moreover, antidepressants display antibacterial properties in the gastrointestinal tract. The aim of this study was to compare the gut microbiota and systemic inflammatory profile of young patients with MDD before and after initiation of antidepressant treatment and/or psychotherapy in comparison with a non-depressed control group (nonMDD).

METHODS

Fecal and blood samples were collected at baseline and at follow-up after four and twelve weeks, respectively. Patients started treatment immediately after collection of the baseline samples. The gut microbiota was characterized by 16 S rRNA gene sequencing targeting the hypervariable V4 region. Plasma levels of 49 unique immune markers were assessed using Mesoscale.

RESULTS

In total, 27 MDD patients and 32 nonMDD controls were included in the study. The gut microbiota in the baseline samples of MDD versus nonMDD participants did not differ regarding α- or β-diversity. However, there was a higher relative abundance of the genera Ruminococcus gnavus group, and a lower relative abundance of the genera Desulfovibrio, Tyzzerella, Megamonas, Olsenella, Gordonibacter, Allisonella and Rothia in the MDD group compared to the nonMDD group. In the MDD group, there was an increase in the genera Rothia, Desulfovibrio, Gordinobacteer and Lactobacillus, while genera belonging to the Firmicutes phylum were found depleted at twelve weeks follow-up compared to baseline. In the MDD group, IL-7, IL-8 and IL-17b levels were elevated compared to the nonMDD group at baseline. Furthermore, MDI score in the MDD group was found to correlate with Bray-Curtis dissimilarity at baseline, and several inflammatory markers at both baseline and after initiation of antidepressant treatment.

CONCLUSION

Several bacterial taxa differed between the MDD group and the nonMDD group at baseline and changed in relative abundance during antidepressant treatment and/or psychotherapy. The MDD group was furthermore found to have a pro-inflammatory profile compared to the nonMDD group at baseline. Further studies are required to investigate the gut microbiota and pro-inflammatory profile of patients with MDD.

Clostridium butyricum Prazmowski can degrade and utilize resistant starch via a set of synergistically acting enzymes

Resistant starch is a prebiotic fiber that is best known for its ability to increase butyrate production by the gut microbiota. This butyrate then plays an important role in modulating the immune system and inflammation. However, the ability to use this resistant starch appears to be a rare trait within the gut microbiota, with only a few species such as Ruminococcus bromii and Bifidobacterium adolescentis having been demonstrated to possess this ability. Furthermore, these bacteria do not directly produce butyrate themselves, rather they rely on cross-feeding interactions with other gut bacteria for its production. Here, we demonstrate that the often-used probiotic organism Clostridium butyricum also possesses the ability to utilize resistant starch from a number of sources, with direct production of butyrate. We further explore the enzymes responsible for this trait, demonstrating that they exhibit significant synergy, though with different enzymes exhibiting more or less importance depending on the source of the resistant starch. Thus, the co-administration of Clostridium butyricum may have the ability to improve the beneficial effects of resistant starch.IMPORTANCEClostridium butyricum is seeing increased use as a probiotic, due to potential health benefits tied to its ability to produce butyrate. Here, we demonstrate that this organism can use a variety of resistant starch sources and characterize the enzymes it uses to accomplish this. Given the relative rarity of resistant starch utilizing ability within the gut and the health benefits tied to resistant starch, the combined use of this organism with resistant starch in synbiotic formulations may prove beneficial.

Serotype-Dependent Inhibition of Streptococcus pneumoniae Growth by Short-Chain Fatty Acids

Streptococcus pneumoniae (pneumococcus) is an opportunistic pathogen that can cause severe infectious diseases such as pneumonia, meningitis, and otitis media. Despite the availability of antibiotics and pneumococcal vaccines against some invasive serotypes, pneumococcal infection remains a tremendous clinical challenge due to the increasing frequency of infection by antimicrobial resistant, nonencapsulated, and/or non-vaccine serotype strains. Short-chain fatty acids (SCFAs), which are produced at various mucosal sites in the body, have potent antimicrobial activity, including inhibition of pathogen growth and/or bacterial biofilm formation. In this study, we investigated the antimicrobial activity of SCFAs (acetate, propionate, and butyrate) against various serotypes pneumococci. Propionate generally inhibited the growth of S. pneumoniae serotypes included in the pneumococcal conjugate vaccine (PCV) 13, except for serotypes 3 and 7F, though butyrate and acetate showed no or low inhibition, depending on the serotypes. Of note, butyrate showed strong inhibition against serotype 3, the most prevalent invasive strain since the introduction of the PCV. No SCFAs showed inhibitory effects against serotype 7F. Remarkably, the nonencapsulated pneumococcal strain had more sensitivity to SCFAs than encapsulated parental strains. Taken together, these results suggest that propionate showing the most potent inhibition of pneumococcal growth may be used as an alternative treatment for pneumococcal infection, and that butyrate could be used against serotype 3, which is becoming a serious threat.

Rye Bran as a Component in the Diets of Lactating Sows-Effects on Sow and Piglet Performance

From a cost and sustainability perspective, the use of by-products such as rye bran in sow diets is of particular interest. Rye bran has valuable ingredients that have potential benefits for the gut health of sows. The aim of this study was to investigate the effects of including 15% rye bran in the sows' feed on the performance of sows and piglets. The feeding started one week before the farrowing date and ended at weaning. Performance was evaluated by measuring sow (n = 175) and piglet body weight (n = 1372) and sows' backfat thickness (n = 80). These data were additionally used to calculate the colostrum intake of the suckling piglets and the sows' milk production. It was found that there were no differences in the performance parameters between the experimental and control groups. However, this study showed that the piglets with light birth weight (LBW (<1000 g)) and medium birth weight (MBW (1000-1500 g) consumed more colostrum when the sows were fed rye bran (LBW: C/R 203.0 ± 39.2 g/214.3 ± 35.9 g; MBW: 291.3 ± 39.0 g/298.5 ± 36.4 g). It can be concluded that including 15% rye bran in the feed of lactating sows has no obvious negative effects on the performance of sows and piglets. Further studies are needed to evaluate the possible positive effects of rye bran.

Butyrate affects bacterial virulence: a new perspective on preventing enteric bacterial pathogen invasion

Enteric bacterial pathogens are a major threat to intestinal health. With the widespread use of antibiotics, bacterial resistance has become a problem, and there is an urgent need for a new treatment to reduce dependence on antibiotics. Butyrate can control enteric bacterial pathogens by regulating the expression of their virulence genes, promoting the posttranslational modification of their proteins, maintaining an anaerobic environment, regulating the host immune system and strengthening the intestinal mucosal barrier. Here, this review describes the mechanisms by which butyrate regulates the pathogenicity of enteric bacterial pathogens from various perspectives and discusses the prospects and limitations of butyrate as a new option for the control of pathogenic bacteria.

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

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

Colonization of chickens with competitive exclusion products results in extensive differences in metabolite composition in cecal digesta

The concept of competitive exclusion is well established in poultry and different products are used to suppress the multiplication of enteric pathogens in the chicken intestinal tract. While the effect has been repeatedly confirmed, the specific principles of competitive exclusion are less clear. The aim of the study was to compare metabolites in the cecal digesta of differently colonized chickens. Metabolites in the cecal contents of chickens treated with a commercial competitive exclusion product or with an experimental product consisting of 23 gut anaerobes or in control untreated chickens were determined by mass spectrometry. Extensive differences in metabolite composition among the digesta of all 3 groups of chickens were recorded. Out of 1,706 detected compounds, 495 and 279 were differently abundant in the chicks treated with a commercial or experimental competitive exclusion product in comparison to the control group, respectively. Soyasaponins, betaine, carnitine, glutamate, tyramine, phenylacetaldehyde, or 3-methyladenine were more abundant in the digesta of control chicks while 4-oxododecanedioic acid, nucleotides, dipeptides, amino acids (except for glutamate), and vitamins were enriched in the digesta of chickens colonized by competitive exclusion products. Metabolites enriched in the digesta of control chicks can be classified as of plant feed origin released in the digesta by degradative activities of the chicken. Some of these molecules disappeared from the digesta of chicks colonized by complex microbiota due to them being metabolized. Instead, nucleotides, amino acids, and vitamins increased in the digesta of colonized chicks as a consequence of the additional digestive potential brought to the cecum by microbiota from competitive exclusion products. It is therefore possible to affect metabolite profiles in the chicken cecum by its colonization with selected bacterial species.

Gut microbes in metabolic disturbances. Promising role for therapeutic manipulations?

The prevalence of overweight, obesity, type 2 diabetes, metabolic syndrome and steatotic liver disease is rapidly increasing worldwide with a huge economic burden in terms of morbidity and mortality. Several genetic and environmental factors are involved in the onset and development of metabolic disorders and related complications. A critical role also exists for the gut microbiota, a complex polymicrobial ecology at the interface of the internal and external environment. The gut microbiota contributes to food digestion and transformation, caloric intake, and immune response of the host, keeping the homeostatic control in health. Mechanisms of disease include enhanced energy extraction from the non-digestible dietary carbohydrates, increased gut permeability and translocation of bacterial metabolites which activate a chronic low-grade systemic inflammation and insulin resistance, as precursors of tangible metabolic disorders involving glucose and lipid homeostasis. The ultimate causative role of gut microbiota in this respect remains to be elucidated, as well as the therapeutic value of manipulating the gut microbiota by diet, pre- and pro- synbiotics, or fecal microbial transplantation.

Contribution of the microbiome for better phenotyping of people living with obesity

Obesity has reached epidemic proportion worldwide and in all ages. Available evidence points to a multifactorial pathogenesis involving gene predisposition and environmental factors. Gut microbiota plays a critical role as a major interface between external factors, i.e., diet, lifestyle, toxic chemicals, and internal mechanisms regulating energy and metabolic homeostasis, fat production and storage. A shift in microbiota composition is linked with overweight and obesity, with pathogenic mechanisms involving bacterial products and metabolites (mainly endocannabinoid-related mediators, short-chain fatty acids, bile acids, catabolites of tryptophan, lipopolysaccharides) and subsequent alterations in gut barrier, altered metabolic homeostasis, insulin resistance and chronic, low-grade inflammation. Although animal studies point to the links between an "obesogenic" microbiota and the development of different obesity phenotypes, the translational value of these results in humans is still limited by the heterogeneity among studies, the high variation of gut microbiota over time and the lack of robust longitudinal studies adequately considering inter-individual confounders. Nevertheless, available evidence underscores the existence of several genera predisposing to obesity or, conversely, to lean and metabolically health phenotype (e.g., Akkermansia muciniphila, species from genera Faecalibacterium, Alistipes, Roseburia). Further longitudinal studies using metagenomics, transcriptomics, proteomics, and metabolomics with exact characterization of confounders are needed in this field. Results must confirm that distinct genera and specific microbial-derived metabolites represent effective and precision interventions against overweight and obesity in the long-term.

Overview of the Mechanistic Potential of Probiotics and Prebiotics in Cancer Chemoprevention

Despite of strides in modern cancer therapeutic strategies, there has not been a successful cure for it until now and prognostic side effects and substantial toxicity to chemotherapy and subsequent homeostatic imbalance remains a major concern for professionals in this field. The significance of the human microbiome in the pathogenesis of cancer is being recognized, documented, and established worldwide. Probiotics and prebiotics are some of the most extensively researched approaches to modulate the microbiota for therapeutic purposes, and research on their potential to prevent and treat cancer has sparked an immense amount of interest. The characteristics of probiotics and prebiotics allow for an array of efficient applications in cancer preventive measures. Probiotics can also be administered coupled with chemotherapy and surgery to alleviate their side effects and help promote the effectiveness of chemotherapeutic drugs. Besides showing promising results they are accompanied by potential risks and controversies that may eventually result in clinical repercussions. This review emphasizes the mechanistic potential and oncosuppressive effects of probiotic and prebiotics through maintenance of intestinal barrier function, modifying innate immune system, immunomodulation, intestinal microbiota metabolism, inhibition of host cell proliferation, preventing pathogen colonization, and exerting selective cytotoxicity against tumor cells.

Butyrate decreases Campylobacter jejuni motility and biofilm partially through influence on LysR expression

The food pathogen Campylobacter jejuni both colonizes the lower intestines of poultry and infects the lower intestines of humans. The lower intestines of both poultry and humans are also home to a wide range of commensal organisms which compete with an organism like C. jejuni for space and resources. The commensal organisms are believed to protect humans against infection by pathogens of the digestive tract like C. jejuni. The short chain fatty acid (SCFA) butyrate is a metabolite commonly produced by commensal organisms within both the poultry and human digestive tract. We investigated the effect that physiologically relevant concentrations of butyrate have on C. jejuni under in vitro conditions. Butyrate at concentrations of 5 and 20 mM negatively impacted C. jejuni motility and biofilm formation. These two traits are believed important for C. jejuni's ability to infect the lower intestines of humans. Additionally, 20 mM butyrate concentrations were observed to influence the expression of a range of different Campylobacter proteins. Constitutive expression of one of these proteins, LysR, within a C. jejuni strain partially lessened the negative influence butyrate had on the bacteria's motility.

CsrA Positively and Directly Regulates the Expression of the pdu, pocR, and eut Genes Required for the Luminal Replication of Salmonella Typhimurium

Enteric pathogens, such as Salmonella, have evolved to thrive in the inflamed gut. Genes located within the Salmonella pathogenicity island 1 (SPI-1) mediate the invasion of cells from the intestinal epithelium and the induction of an intestinal inflammatory response. Alternative electron acceptors become available in the inflamed gut and are utilized by Salmonella for luminal replication through the metabolism of propanediol and ethanolamine, using the enzymes encoded by the pdu and eut genes. The RNA-binding protein CsrA inhibits the expression of HilD, which is the central transcriptional regulator of the SPI-1 genes. Previous studies suggest that CsrA also regulates the expression of the pdu and eut genes, but the mechanism for this regulation is unknown. In this work, we show that CsrA positively regulates the pdu genes by binding to the pocR and pduA transcripts as well as the eut genes by binding to the eutS transcript. Furthermore, our results show that the SirA-CsrB/CsrC-CsrA regulatory cascade controls the expression of the pdu and eut genes mediated by PocR or EutR, which are the positive AraC-like transcriptional regulators for the pdu and eut genes, respectively. By oppositely regulating the expression of genes for invasion and for luminal replication, the SirA-CsrB/CsrC-CsrA regulatory cascade could be involved in the generation of two Salmonella populations that cooperate for intestinal colonization and transmission. Our study provides new insight into the regulatory mechanisms that govern Salmonella virulence. IMPORTANCE The regulatory mechanisms that control the expression of virulence genes are essential for bacteria to infect hosts. Salmonella has developed diverse regulatory mechanisms to colonize the host gut. For instance, the SirA-CsrB/CsrC-CsrA regulatory cascade controls the expression of the SPI-1 genes, which are required for this bacterium to invade intestinal epithelium cells and for the induction of an intestinal inflammatory response. In this study, we determine the mechanisms by which the SirA-CsrB/CsrC-CsrA regulatory cascade controls the expression of the pdu and eut genes, which are necessary for the replication of Salmonella in the intestinal lumen. Thus, our data, together with the results of previous reports, indicate that the SirA-CsrB/CsrC-CsrA regulatory cascade has an important role in the intestinal colonization by Salmonella.

Rye and Rye Bran as Components of Diets in Piglet Production-Effects on Salmonella Prevalence

The nutritional benefits of rye (and therefore rye bran) are mainly due to its high content of fermentable dietary fiber, the non-starch polysaccharides (NSP). Microorganisms in the large intestine are able to convert these into short-chain fatty acids (SCFA), including butyrate. Butyrate strengthens the epithelial barrier function in the colon by nourishing the enterocytes and inhibiting the spread of Salmonella in the intestinal tract. Therefore, the aim of this study was to test under field conditions whether a diet with rye or rye bran as the main ingredient for gilts, sows, and weaned piglets is associated with a lower Salmonella prevalence. Depending on the age groups, between 20-30% rye or between 15-20% rye bran was used in the experimental group. A total of n = 1983 boot swabs, n = 356 fecal samples, and n = 1909 serum samples were examined. The results of this study show that rye or rye bran at the levels used had no apparent effect on the number of positive Salmonella samples. However, the Salmonella OD values in the experimental groups were significantly lower than in the control group. This suggests that the use of rye leads to a lower incidence of infection, but this effect could not be proven from swabs.

Effects of substituting wheat by rye in diets for young fattening pigs on nutrient digestibility, performance, products of intestinal fermentation, and fecal characteristics

Climate change and increasing demands to reduce the environmental impact of feed production are major challenges for animal nutritionists. Compared to wheat, which is commonly used in high levels in European piglet diets, rye is more efficient in using limited resources, most importantly, water and phosphorus. As a result, its cultivation has a relatively low carbon footprint. The high amounts of non-starch polysaccharides of rye might lead to an increased intestinal fermentation with potential beneficial effects on gut health. However, the high levels of non-starch polysaccharides in rye, which have a major impact on the physico-chemical conditions of the digesta, might affect digestibility and performance especially in young animals. It was therefore of interest to compare the effects of isoenergetic diets with increasing levels of rye as a replacement for wheat fed to young fattening pigs (bodyweight: 16-40 kg). The control diet contained 69% of wheat, while in the other three experimental diets, the amount of wheat was gradually replaced (by a third in each case) with rye. Thus, the experimental diets contained 23, 46, and 69% of rye. A total of 40 young pigs were housed individually in four dietary treatment groups. During a 4 week trial, effects on performance, digestibility, products of intestinal fermentation, and fecal characteristics were evaluated. There were no negative effects on feed intake and gains, even though the feed conversion ratio increased with the highest dietary rye level (69%). Digestibility rates of organic matter and crude protein did not differ significantly. Without affecting the characteristics of the feces, numerically higher amounts of intestinal fermentation products and higher colonic digesta mass were observed.

Formate Metabolism in Shigella flexneri and Its Effect on HeLa Cells at Different Stages during the Infectious Process

Shigellosis caused by Shigella is one of the most important foodborne illnesses in global health, but little is known about the metabolic cross talk between this bacterial pathogen and its host cells during the different stages of the infection process. A detailed understanding of the metabolism can potentially lead to new drug targets remedying the pressing problem of antibiotic resistance. Here, we use stable isotope-resolved metabolomics as an unbiased and fast method to investigate how Shigella metabolizes 13C-glucose in three different environments: inside the host cells, adhering to the host cells, and alone in suspension. We find that especially formate metabolism by bacteria is sensitive to these different environments. The role of formate in pathogen metabolism is sparsely described in the literature compared to the roles of acetate and butyrate. However, its metabolic pathway is regarded as a potential drug target due to its production in microorganisms and its absence in humans. Our study provides new knowledge about the regulatory effect of formate. Bacterial metabolism of formate is pH dependent when studied alone in culture medium, whereas this effect is less pronounced when the bacteria adhere to the host cells. Once the bacteria are inside the host cells, we find that formate accumulation is reduced. Formate also affects the host cells resulting in a reduced infection rate. This was correlated to an increased immune response. Thus, intriguingly formate plays a double role in pathogenesis by increasing the virulence of Shigella and at the same time stimulating the immune response of the host. IMPORTANCE Bacterial infection is a pressing societal concern due to development of resistance toward known antibiotics. Central carbon metabolism has been suggested as a potential new target for drug development, but metabolic changes upon infection remain incompletely understood. Here, we used a cellular infection model to study how the bacterial pathogen Shigella adapts its metabolism depending on the environment starting from the extracellular medium until Shigella successfully invaded and proliferated inside host cells. The mixed-acid fermentation of Shigella was the major metabolic pathway during the infectious process, and the glucose-derived metabolite formate surprisingly played a divergent role in the pathogen and in the host cell. Our data show reduced infection rate when both host cells and bacteria were treated with formate, which correlated with an upregulated immune response in the host cells. The formate metabolism in Shigella thus potentially provides a route toward alternative treatment strategies for Shigella prevention.

Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation

BACKGROUND

In the pig production, diarrhea can occur during different growth stages including the period 4-16 weeks post weaning, during which a diarrheal outbreak also termed as colitis-complex diarrhea (CCD) can occur and it is distinct from post-weaning diarrhea (1-2 weeks post weaning). We hypothesized that CCD in growing pigs is associated with changes in colonic microbiota composition and fermentation patterns, and the aim of the present observational study was to identify changes in digesta-associated bacteria (DAB) and mucus-associated bacteria (MAB) in the colon of growing pigs with and without diarrhea. A total number of 30 pigs (8, 11, and 12 weeks of age) were selected; 20 showed clinical signs of diarrhea and 10 appeared healthy. Based on histopathological examination of colonic tissues, 21 pigs were selected for further studies and classified as follows: without diarrhea, no colon inflammation (NoDiar; n = 5), with diarrhea, without colonic inflammation (DiarNoInfl; n = 4), and with diarrhea, with colonic inflammation (DiarInfl; n = 12). Composition (based on 16S rRNA gene amplicon sequencing) and fermentation pattern (short-chain fatty acids; SCFA profile) of the DAB and MAB communities were characterized.

RESULTS

The DAB showed higher alpha diversity compared to MAB in all pigs, and both DAB and MAB showed lowest alpha diversity in the DiarNoInfl group. Beta diversity was significantly different between DAB and MAB as well as between diarrheal groups in both DAB and MAB. Compared to NoDiar, DiarInfl showed increased abundance of various taxa, incl. certain pathogens, in both digesta and mucus, as well as decreased digesta butyrate concentration. However, DiarNoInfl showed reduced abundance of different genera (mainly Firmicutes) compared to NoDiar, but still lower butyrate concentration.

CONCLUSION

Diversity and composition of MAB and DAB changed in diarrheal groups depending on presence/absence of colonic inflammation. We also suggest that DiarNoInfl group was at the earlier stage of diarrhea compared with DiarInfl, with a link to dysbiosis of colonic bacterial composition as well as reduced butyrate concentration, which plays a pivotal role in gut health. This could have led to diarrhea with inflammation due to a dysbiosis, associated with an increase in e.g., Escherichia-Shigella (Proteobacteria), Helicobacter (Campylobacterota), and Bifidobacterium (Actinobacteriota), which may tolerate or utilize oxygen and cause epithelial hypoxia and inflammation. The increased consumption of oxygen in epithelial mucosal layer by infiltrated neutrophils may also have added up to this hypoxia. Overall, the results confirmed that changes in DAB and MAB were associated with CCD and reduced butyrate concentration in digesta. Moreover, DAB might suffice for future community-based studies of CCD.

The microbiome and rheumatic heart disease: current knowledge and future perspectives

Rheumatic heart disease (RHD) is a cardiovascular disease caused by an autoimmune response to group A Streptococcus (GAS) infection resulting in the damage of heart valves. RHD is the most commonly acquired heart disease among children and young adults with a global burden of over 40 million cases accounting for 306,000 deaths annually. Inflammation in the heart valves caused due to molecular mimicry between the GAS antigens and host cardiac proteins is facilitated by cytokines, cross-reactive antibodies and CD4⁺ T cells. The complex interaction between genetic and environmental factors linked with erratic events leads to the loss of immunological tolerance and autoimmunity in RHD. Despite extensive research on the etiopathogenesis of RHD, the precise mechanism underpinning the initiation of acute rheumatic fever (ARF) to the progression of RHD still remains elusive. Mounting evidences support the contribution of the human microbiome in the development of several immune-mediated diseases including rheumatoid arthritis, juvenile idiopathic arthritis, Kawasaki disease, inflammatory bowel disease and type 1 diabetes. The microbiome and their metabolites could play a crucial role in the integrity of the epithelial barrier, development of the immune system, inflammation and differentiation of T cell subsets. Consequently, microbiome dysbiosis might result in autoimmunity by molecular mimicry, epitope spreading and bystander activation. This review discusses various aspects of the interaction between the microbiome and the immune system in order to reveal causative links relating dysbiosis and autoimmune diseases with special emphasis on RHD.

Salmonella Invasion Is Controlled by Competition among Intestinal Chemical Signals

The intestine is a complex, ever-changing environment replete with an array of signaling molecules. To colonize such a complex organ, pathogens have adapted to utilize specific cues from the local environment to intricately regulate the expression of their virulence determinants. Salmonella preferentially colonizes the distal ileum, a niche enriched in the metabolite formic acid. Here, we show that the relatively higher concentration of this metabolite in the distal ileum prevents other signals from repressing Salmonella invasion in that region. We show that imported and unmetabolized formic acid functions as a cytoplasmic signal that competitively binds to HilD, the master transcriptional regulator of Salmonella invasion, thus preventing repressive fatty acids from binding to the protein. This results in an increased lifetime of HilD and subsequent derepression of invasion genes. This study demonstrates an important mechanism by which Salmonella utilizes competition among signals in the gut to its advantage as a pathogen. IMPORTANCE Enteric pathogens acutely sense their environment for signals to regulate their virulence functions. We demonstrate here that the enteric pathogen Salmonella utilizes the competition among certain regional intestinal constituents to modulate its virulence determinants in that region. We show that the high concentration of formic acid in the ileum outcompetes other signals and triggers the activation of virulence genes in the ileum. This study shows a delicate spatial and temporal mechanism by which enteric pathogens may utilize the competition among environmental cues to optimize their pathogenicity.

Sodium butyrate supplementation impacts the gastrointestinal bacteria of dairy calves before weaning

The objective of this study was to systematically investigate how sodium butyrate (SB) affects the gastrointestinal bacteria in newborn calves at different stages before weaning. Forty female newborn Holstein calves (4-day-old, 40 ± 5 kg of body weight) were randomly divided into four groups; each group was supplemented with four SB doses: 0, 15, 30, and 45 g/day (ten replicates) in SB0, SB15, SB30, and SB45 groups, respectively. SB was fed with milk replacer from day 4 to day 60. Rumen fluid and feces were collected on days 2, 14, 28, 42, and 60 for 16S rRNA high-throughput sequencing. Data were analyzed in a complete randomized design and analyzed on the online platform of Majorbio Cloud Platform. The results showed that SB significantly increased the α-diversity in feces, especially Shannon and Chao indices in SB45 and SB30 at day 60 more than in SB15 (P < 0.05). Additionally, SB significantly enhanced Firmicutes growth from day 2 to 28 and also increased Bacteroides abundance from day 28 to 42 in rumen and feces (P < 0.05). SB also significantly inhibited Proteobacteria abundance in rumen and feces during the study period (P < 0.05). SB also promoted some potential beneficial bacterial abundance, including Prevotella, Lachnospiraceae, Clostridium, Ruminococcus, and Muribaculaceae (P < 0.05). Additionally, Escherichia-Shigella abundance at SB0 was significantly lower than in the other groups (P < 0.05). In conclusion, this study firstly reported a dynamic curve showing of the SB effects on bacteria in calves before weaning. This study provides valuable evidence for the development of the gastrointestinal tract of the calves in the early stage of the life. SB supplementation improved the gastrointestinal health by regulating the bacterial populations. KEY POINTS: • The gastrointestinal tract of calves has been improved after the SB supplementation. • Microbes were the vital influential factor in the development of calves. • Intervention before weaning is an effective strategy for calf health.

Metabolite interactions between host and microbiota during health and disease: Which feeds the other?

Metabolites produced by the host and microbiota play a crucial role in how human bodies develop and remain healthy. Most of these metabolites are produced by microbiota and hosts in the digestive tract. Metabolites in the gut have important roles in energy metabolism, cellular communication, and host immunity, among other physiological activities. Although numerous host metabolites, such as free fatty acids, amino acids, and vitamins, are found in the intestine, metabolites generated by gut microbiota are equally vital for intestinal homeostasis. Furthermore, microbiota in the gut is the sole source of some metabolites, including short-chain fatty acids (SCFAs). Metabolites produced by microbiota, such as neurotransmitters and hormones, may modulate and significantly affect host metabolism. The gut microbiota is becoming recognized as a second endocrine system. A variety of chronic inflammatory disorders have been linked to aberrant host-microbiota interplays, but the precise mechanisms underpinning these disturbances and how they might lead to diseases remain to be fully elucidated. Microbiome-modulated metabolites are promising targets for new drug discovery due to their endocrine function in various complex disorders. In humans, metabolotherapy for the prevention or treatment of various disorders will be possible if we better understand the metabolic preferences of bacteria and the host in specific tissues and organs. Better disease treatments may be possible with the help of novel complementary therapies that target host or bacterial metabolism. The metabolites, their physiological consequences, and functional mechanisms of the host-microbiota interplays will be highlighted, summarized, and discussed in this overview.

A high-sucrose diet causes microbiota composition shift and promotes the susceptibility of mice to Salmonella Typhimurium infection

A westernized diet characterized by high fat and sugar is tightly associated with the development of metabolic diseases and inflammatory bowel disease. Although a high-fat diet has been extensively studied for its involvement in various diseases, fewer studies have examined the impact of a high-sugar diet on the development of certain diseases, particularly enteric infections. This study aimed to explore the effect of a high sucrose diet on Salmonella Typhimurium-induced infection. C57BL/6 mice received a normal diet (Control) or a high sucrose diet (HSD) for eight weeks and then were infected by Salmonella Typhimurium. The high-sugar diet profoundly altered the relative abundance of certain microbial taxa. Bacteroidetes and Verrucomicrobiota were more abundant in normal diet-fed mice than in HSD-fed mice. Moreover, short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were significantly higher in mice from the control group than the HSD group. More S. Typhimurium counts in feces and other tissues were observed in HSD-fed mice after infection. Tight junction proteins and antimicrobial peptides were significantly decreased in HSD-fed mice. Fecal microbiota transplantation (FMT) demonstrated that mice that received normal fecal microbiota had lower Salmonella Typhimurium burdens compared with mice that received HSD fecal microbiota, indicating that the altered microbial communities are associated with the severity of infection. Together, these findings suggest that the excessive intake of sucrose disturbs intestinal homeostasis and predisposes mice to Salmonella-induced infection.

Glucose oxidase as an alternative to antibiotic growth promoters improves the immunity function, antioxidative status, and cecal microbiota environment in white-feathered broilers

This study aimed to demonstrate the effects of glucose oxidase (GOD) on broilers as a potential antibiotic substitute. A total of four hundred twenty 1-day-old male Cobb500 broilers were randomly assigned into five dietary treatments, each with six replicates (12 chicks per replicate). The treatments included two control groups (a basal diet and a basal diet with 50 mg/kg aureomycin) and three GOD-additive groups involving three different concentrations of GOD. Analysis after the t-test showed that, on day 21, the feed:gain ratio significantly decreased in the 1,200 U/kg GOD-supplied group (GOD1200) compared to the antibiotic group (Ant). The same effect was also observed in GOD1200 during days 22-42 and in the 600 U/kg GOD-supplied group (GOD600) when compared to the control group (Ctr). The serum tests indicated that, on day 21, the TGF-β cytokine was significantly decreased in both GOD600 and GOD1200 when compared with Ctr. A decrease in malondialdehyde and an increase in superoxide dismutase in GOD1200 were observed, which is similar to the effects seen in Ant. On day 42, the D-lactate and glutathione peroxidase activity changed remarkably in GOD1200 and surpassed Ant. Furthermore, GOD upregulated the expression of the jejunal barrier genes (MUC-2 and ZO-1) in two phases relative to Ctr. In the aureomycin-supplied group, the secretory immunoglobulin A significantly decreased in the jejunum at 42 days. Changes in microbial genera were also discovered in the cecum by sequencing 16S rRNA genes at 42 days. The biomarkers for GOD supplementation were identified as Colidextribacter, Oscillibacter, Flavonifractor, Oscillospira, and Shuttleworthia. Except for Shuttleworthia, all the abovementioned genera were n-butyrate producers known for imparting their various benefits to broilers. The PICRUSt prediction of microbial communities revealed 11 pathways that were enriched in both the control and GOD-supplied groups. GOD1200 accounted for an increased number of metabolic pathways, demonstrating their potential in aiding nutrient absorption and digestion. In conclusion, a diet containing GOD can be beneficial to broiler health, particularly at a GOD concentration of 1,200 U/kg. The improved feed conversion ratio, immunity, antioxidative capacity, and intestinal condition demonstrated that GOD could be a valuable alternative to antibiotics in broiler breeding.

Timing and delivery route effects of cecal microbiome transplants on Salmonella Typhimurium infections in chickens: potential for in-hatchery delivery of microbial interventions

BACKGROUND

Exposure to microbes early in life has long-lasting effects on microbial community structure and function of the microbiome. However, in commercial poultry settings chicks are reared as a single-age cohort with no exposure to adult birds which can have profound effects on microbiota development and subsequent pathogen challenge. Microbiota manipulation is a proven and promising strategy to help reduce pathogen load and transmission within broiler flocks. However, administration of microbiota transplant products in a hatchery setting may prove challenging. Effective administration strategies are dependent on key factors, such as; the age of chicks receiving interventions and mode of delivery. This study aimed to assess these two aspects to provide supporting evidence towards microbiome manipulation strategies for use in commercial hatcheries.

RESULTS

Manipulation of the microbiota between 4 and 72 h of hatch markedly reduced faecal shedding and colonisation with the foodborne pathogen Salmonella enterica serovar Typhimurium (ST4/74). Administration of transplant material via spray or gel drop delivery systems had minimal effect on the protection conferred with fewer birds in transplant groups shown to shed ST4/74 in the faeces compared to PBS-gavaged control birds. Analysis of the microbiome following transplantation demonstrated that all transplant groups had higher diversity and species richness than non-transplant groups during the first week of life and the early stages of infection with ST47/4.The relative abundance of the bacterium Faecalibacterium prausnitzii was significantly higher in CMT groups compared to PBS controls. The presence of F. prausnitzii was also shown to increase in PBS-challenged birds compared to unchallenged birds potentially indicating a role of this bacterium in limiting Salmonella infections.

CONCLUSIONS

This study demonstrated that administration of microbiome transplants, using methods that would align with hatchery practices, effectively reduced colonisation and shedding of Salmonella in chickens. Age of chicks at microbiome administration had limited effect on the diversity and composition of the microbiome and conferred protection against Salmonella infections. Traditional hatchery delivery systems, such as spray or gel-drop, are sufficient to transfer donor material, alter the microbiome and confer protection against Salmonella. This study helps highlight the opportunity for use of microbiome modification methods within the hatchery.

Interbacterial Chemical Communication-Triggered Nascent Proteomics

Metabolic labeling with clickable noncanonical amino acids has enabled nascent proteome profiling, which can be performed in a cell-type-specific manner. However, nascent proteomics in an intercellular communication-dependent manner remains challenging. Here we develop communication-activated profiling of protein expression (CAPPEX), which integrates the LuxI/LuxR quorum sensing circuit with the cell-type-specific nascent proteomics method to enable selective click-labeling of newly synthesized proteins in a specific bacterium upon receiving chemical signals from another reporter bacterium. CAPPEX reveals that E. coli competes with Salmonella for tryptophan as the precursor for indole, and the resulting indole suppressed the expression of virulence factors in Salmonella. This tryptophan-indole axis confers attenuation of Salmonella invasion in host cells and living mice. The CAPPEX strategy should be widely applicable for investigating various interbacterial communication processes.

Navigating Environmental Transitions: the Role of Phenotypic Variation in Bacterial Responses

The ability of bacteria to respond to changes in their environment is critical to their survival, allowing them to withstand stress, form complex communities, and induce virulence responses during host infection. A remarkable feature of many of these bacterial responses is that they are often variable across individual cells, despite occurring in an isogenic population exposed to a homogeneous environmental change, a phenomenon known as phenotypic heterogeneity. Phenotypic heterogeneity can enable bet-hedging or division of labor strategies that allow bacteria to survive fluctuating conditions. Investigating the significance of phenotypic heterogeneity in environmental transitions requires dynamic, single-cell data. Technical advances in quantitative single-cell measurements, imaging, and microfluidics have led to a surge of publications on this topic. Here, we review recent discoveries on single-cell bacterial responses to environmental transitions of various origins and complexities, from simple diauxic shifts to community behaviors in biofilm formation to virulence regulation during infection. We describe how these studies firmly establish that this form of heterogeneity is prevalent and a conserved mechanism by which bacteria cope with fluctuating conditions. We end with an outline of current challenges and future directions for the field. While it remains challenging to predict how an individual bacterium will respond to a given environmental input, we anticipate that capturing the dynamics of the process will begin to resolve this and facilitate rational perturbation of environmental responses for therapeutic and bioengineering purposes.

Propionate and Butyrate Inhibit Biofilm Formation of Salmonella Typhimurium Grown in Laboratory Media and Food Models

Salmonella is among the most frequently isolated foodborne pathogens, and biofilm formed by Salmonella poses a potential threat to food safety. Short-chain fatty acids (SCFAs), especially propionate and butyrate, have been demonstrated to exhibit a beneficial effect on promoting intestinal health and regulating the host immune system, but their anti-biofilm property has not been well studied. This study aims to investigate the effects of propionate or butyrate on the biofilm formation and certain virulence traits of Salmonella. We investigated the effect of propionate or butyrate on the biofilm formation of Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344 grown in LB broth or food models (milk or chicken juice) by crystal violet staining methods. Biofilm formation was significantly reduced in LB broth and food models and the reduction was visualized using a scanning electron microscope (SEM). Biofilm metabolic activity was attenuated in the presence of propionate or butyrate. Meanwhile, both SCFAs decreased AI-2 quorum sensing based on reporter strain assay. Butyrate, not propionate, could effectively reduce bacterial motility. Bacterial adhesion to and invasion of Caco-2 cells were also significantly inhibited in the presence of both SCFAs. Finally, two SCFAs downregulated virulence genes related to biofilm formation and invasion through real-time polymerase chain reaction (RT-PCR). These findings demonstrate the potential application of SCFAs in the mitigation of Salmonella biofilm in food systems, but future research mimicking food environments encountered during the food chain is necessitated.

Potential of gut-derived short-chain fatty acids to control enteric pathogens

Short-chain fatty acids (SCFAs) are a very important group of metabolites located in the gut that play a crucial role in the regulation of gut function and pathogen resistance. Since many enteric pathogens respond differently to various SCFAs, substantial efforts have been made to understand the regulatory effects of SCFA types on enteric pathogens. The application of protein post-translational modifications (PTMs) in bacterial research provides a new perspective for studying the regulation of enteric pathogens by different SCFAs. Existing evidence suggests that the SCFAs acetate, propionate, and butyrate influence bacterial processes by extensively promoting the acylation of key bacterial proteins. SCFAs can also prevent the invasion of pathogenic bacteria by regulating the barrier function and immune status of the host gut. In this review, we describe the mechanisms by which different SCFAs modulate the pathogenicity of enteric pathogens from multiple perspectives. We also explore some recent findings on how enteric pathogens counteract SCFA inhibition. Lastly, we discuss the prospects and limitations of applying SCFAs to control enteric pathogens.

In vitro evaluation of sodium butyrate on the growth of three Salmonella serovars derived from pigs at a mild acidic pH value

Foodborne zoonotic diseases can be transferred into the food chain at the stage of livestock farming. As an emerging public health challenge, practicable reduction measures in porcine health management for Salmonella are constantly being investigated. This in vitro study aimed to determine the influence of six different sodium butyrate (SB) concentrations (0, 5, 10, 20, 40, and 80 mM) on the growth of three different Salmonella enterica serovars at a constant pH value of 6.0, corresponding to conditions in the pig's hindgut. S. Derby and S. Typhimurium, isolated from a pig farm, and S. Typhimurium DSM 19587, which served as control, were used. Broth microdilution assay was applied to record Salmonella growth in the presence of different SB-concentrations over six different incubation periods (0, 1, 2, 4, 6, and 24 h). Results were quantified in the log colony-forming units (log10 CFU/mL). For 1 h incubation, the addition of SB showed no significant differences in the range of initial Salmonella dose of about 5.7 log10 between concentrations (0-80 mM, 5.26 ± 0.10-5.60 ± 0.07 log10, p > 0.05). After 6 h, for SB addition, the range of Salmonella counts was significantly lower compared to no addition of SB (5-80 mM, p < 0.05), 6.78 ± 0.84-7.90 ± 0.10 log10 for 5 mM, and 7.53 ± 0.04-8.71 ± 0.22 log10 for 0 mM. Moreover, for SB concentrations of 40 and 80 mM, no difference in the range of Salmonella counts over 6 h was obtained (5.23 ± 0.11-5.38 ± 0.05 log10, p > 0.05), and minor Salmonella growth was recorded at the earliest after 24 h incubation. Growth rates for varying SB concentrations and incubation times were confirmed in a similar manner for the three serovars. Obtained results suggest that increasing SB concentrations suppress Salmonella growth for concentrations of 5-20 mM over a 6 h incubation period and for 40 and 80 mM over a 24 h incubation period. When transferring these in vitro findings to the porcine organism, it may be assumed that Salmonella reduction can be achieved by increased butyrate content in the chyme of the large intestine.

Vitamin B12 coordinates ileal epithelial cell and microbiota functions to resist Salmonella infection in mice

Deprivation of vitamin B12 (VB12) is linked to various diseases, but the underlying mechanisms in disease progression are poorly understood. Using multiomic approaches, we elucidated the responses of ileal epithelial cells (iECs) and gut microbiome to VB12 dietary restriction. Here, VB12 deficiency impaired the transcriptional and metabolic programming of iECs and reduced epithelial mitochondrial respiration and carnitine shuttling during intestinal Salmonella Typhimurium (STm) infection. Fecal microbial and untargeted metabolomic profiling identified marked changes related to VB12 deficiency, including reductions of metabolites potentially activating mitochondrial β-oxidation in iECs and short-chain fatty acids (SCFAs). Depletion of SCFA-producing microbes by streptomycin treatment decreased the VB12-dependent STm protection. Moreover, compromised mitochondrial function of iECs correlated with declined cell capability to utilize oxygen, leading to uncontrolled oxygen-dependent STm expansion in VB12-deficient mice. Our findings uncovered previously unrecognized mechanisms through which VB12 coordinates ileal epithelial mitochondrial homeostasis and gut microbiota to regulate epithelial oxygenation, resulting in the control of aerobic STm infection.

Long Chain Fatty Acids and Virulence Repression in Intestinal Bacterial Pathogens

When bacterial pathogens enter the gut, they encounter a complex milieu of signaling molecules and metabolites produced by host and microbial cells or derived from external sources such as the diet. This metabolomic landscape varies throughout the gut, thus establishing a biogeographical gradient of signals that may be sensed by pathogens and resident bacteria alike. Enteric bacterial pathogens have evolved elaborate mechanisms to appropriately regulate their virulence programs, which involves sensing and responding to many of these gut metabolites to facilitate successful gut colonization. Long chain fatty acids (LCFAs) represent major constituents of the gut metabolome that can impact bacterial functions. LCFAs serve as important nutrient sources for all cellular organisms and can function as signaling molecules that regulate bacterial metabolism, physiology, and behaviors. Moreover, in several enteric pathogens, including Salmonella enterica, Listeria monocytogenes, Vibrio cholerae, and enterohemorrhagic Escherichia coli, LCFA sensing results in the transcriptional repression of virulence through two general mechanisms. First, some LCFAs function as allosteric inhibitors that decrease the DNA binding affinities of transcriptional activators of virulence genes. Second, some LCFAs also modulate the activation of histidine kinase receptors, which alters downstream intracellular signaling networks to repress virulence. This mini-review will summarize recent studies that have investigated the molecular mechanisms by which different LCFA derivatives modulate the virulence of enteric pathogens, while also highlighting important gaps in the field regarding the roles of LCFAs as determinants of infection and disease.

A review on anticancer, antibacterial and photo catalytic activity of various nanoparticles synthesized by probiotics

Probiotics are beneficial bacteria that have a significant effect on host health and they are widely used in preventing and treating diseases. Nowadays probiotics are present in food, drug and several commercial complement products. In recent years the use of probiotics in the nanotechnology area, especially in nanoparticle synthesis, has significantly been increased. In this review, after some introduction about probiotic and their advantages, all the nanoparticles produced by probiotics are reviewed and discussed. Furthermore, biosynthetic mechanisms of nanoparticles and its applications in cancer therapy, antibacterial and photo catalytic activities, are also discussed.

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

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

Chemical proteomics for identifying short-chain fatty acid modified proteins in Salmonella

Microbiota-metabolized small molecules play important roles to regulate host immunity and pathogen virulence. Specifically, microbiota generates millimolar concentration of short-chain fatty acid (SCFA) that can directly inhibit Salmonella virulence. Here, we describe chemical proteomic methods to identify SCFA-modified proteins in Salmonella using free fatty acids as well as their salicylic acid derivatives. In addition, we include CRISPR-Cas9 gene editing protocols for epitope-tagging of specific proteins to validate SCFA-modification in Salmonella. These protocols should facilitate the discovery and functional analysis of SCFA-modified proteins in Salmonella microbiology and pathogenesis.

Effect of diet on pathogen performance in the microbiome

Intricate interactions among commensal bacteria, dietary substrates and immune responses are central to defining microbiome community composition, which plays a key role in preventing enteric pathogen infection, a dynamic phenomenon referred to as colonisation resistance. However, the impact of diet on sculpting microbiota membership, and ultimately colonisation resistance has been overlooked. Furthermore, pathogens have evolved strategies to evade colonisation resistance and outcompete commensal microbiota by using unique nutrient utilisation pathways, by exploiting microbial metabolites as nutrient sources or by environmental cues to induce virulence gene expression. In this review, we will discuss the interplay between diet, microbiota and their associated metabolites, and how these can contribute to or preclude pathogen survival.

Impact of bacterial infection and intestinal microbiome on colorectal cancer development

ABSTRACT

Accumulating evidence suggests that intestinal bacteria play an important role in the pathogenesis of colorectal cancer (CRC). Due to the complexity of the intestinal microbiome, identification of the specific causative microbial agents in CRC remains challenging, and the search for the causative microbial agents is intense. However, whether bacteria or their products can induce inflammation that results in tumorigenesis or directly causes CRC in humans is still not clear. This review will mainly focus on the progress of bacterial infection and CRC, and introduce the microbial contribution to the hallmarks of cancer. This article uses Salmonella and its chronic infection as an example to investigate a single pathogen and its role in the development of CRC, based on laboratory and epidemiological evidence. The bacterial infection leads to an altered intestinal microbiome. The review also discusses the dysfunction of the microbiome and the mechanism of host-microbial interactions, for example, bacterial virulence factors, key signaling pathways in the host, and microbial post-translational modifications in the tumorigenesis. Colonic carcinogenesis involves a progressive accumulation of mutations in a genetically susceptible host leading to cellular autonomy. Moving forward, more human data are needed to confirm the direct roles of bacterial infection in CRC development. Insights into the inhibiting infection will help to prevent cancer and develop strategies to restore the balance between host and microorganisms.

The Role of Gut Microbiota and Metabolites in Obesity-Associated Chronic Gastrointestinal Disorders

The gut microbiota is a complex community of microorganisms that has become a new focus of attention due to its association with numerous human diseases. Research over the last few decades has shown that the gut microbiota plays a considerable role in regulating intestinal homeostasis, and disruption to the microbial community has been linked to chronic disease conditions such as inflammatory bowel disease (IBD), colorectal cancer (CRC), and obesity. Obesity has become a global pandemic, and its prevalence is increasing worldwide mostly in Western countries due to a sedentary lifestyle and consumption of high-fat/high-sugar diets. Obesity-mediated gut microbiota alterations have been associated with the development of IBD and IBD-induced CRC. This review highlights how obesity-associated dysbiosis can lead to the pathogenesis of IBD and CRC with a special focus on mechanisms of altered absorption of short-chain fatty acids (SCFAs).

Closely related Salmonella Derby strains triggered distinct gut microbiota alteration

Background

Salmonella Derby is one of the most predominant Salmonella serotypes that seriously threatens food safety. This bacterium can be further differentiated to sub-populations with different population sizes; however, whether and how the S. Derby–gut microbiota interactions affect epidemic patterns of S. Derby sub-populations remain largely unknown.

Results

We selected two representative strains, 14T and 14C, which represent rarely distributed and prevalent sub-populations of the S. Derby ST40 group, respectively, to address this question using a mouse model. Effects of oral administration of both strains was monitored for 14 days. Alpha diversity of gut microbiota at early stages of infection (4 h post infection) was higher in 14C-treated mice and lower in 14T-treated mice compared with controls. Strain 14T triggered stronger inflammation responses but with lower pathogen titer in spleen compared with strain 14C at 14 days post infection. Certain known probiotic bacteria that can hinder colonization of Salmonella, such as Bifidobacteriaceae and Akkermansiaceae, exhibited increased relative abundance in 14T-treated mice compared with 14C-treated mice. Our results also demonstrated that Ligilactobacillus strains isolated from gut microbiota showed stronger antagonistic activity against strain 14T compared with strain 14C.

Conclusions

We identified how S. Derby infection affected gut microbiota composition, and found that the 14T strain, which represented a rarely distributed S. Derby sub-population, triggered stronger host inflammation responses and gut microbiota disturbance compared with the 14C strain, which represented a prevalent S. Derby sub-population. This study provides novel insights on the impacts of gut microbiota on the epidemic patterns of Salmonella populations.

Dual role of microbiota-derived short-chain fatty acids on host and pathogen

A growing body of documents shows microbiota produce metabolites such as short-chain fatty acids (SCFAs) as crucial executors of diet-based microbial influence the host and bacterial pathogens. The production of SCFAs depends on the metabolic activity of intestinal microflora and is also affected by dietary changes. SCFAs play important roles in maintaining colonic health as an energy source, as a regulator of gene expression and cell differentiation, and as an anti-inflammatory agent. Additionally, the regulated expression of virulence genes is critical for successful infection by an intestinal pathogen. Bacteria rely on sensing environmental signals to find preferable niches and reach the infectious state. This review will present data supporting the diverse functional roles of microbiota-derived butyrate, propionate, and acetate on host cellular activities such as immune modulation, energy metabolism, nervous system, inflammation, cellular differentiation, and anti-tumor effects, among others. On the other hand, we will discuss and summarize data about the role of these SCFAs on the virulence factor of bacterial pathogens. In this regard, receptors and signaling routes for SCFAs metabolites in host and pathogens will be introduced.