Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak

Carbapenemase-producing Enterobacterales and their carbapenemase genes are stably recovered across the wastewater-watershed ecosystem nexus

Carbapenemase-producing Enterobacterales (CPE) have emerged as an important nosocomial threat to hospitalized patients, but CPE can also colonize the enteric microbiota of healthy individuals in the community. We hypothesized that clinically relevant CPE are frequently transported in municipal wastewater flows to treatment plants where they are reduced but not eliminated and are subsequently discharged into nearby surface waters and disseminate in the environment. We sampled untreated influent, treated effluent, and nearby surface waters weekly for a one-year period at a single large metropolitan wastewater treatment plant (WWTP) servicing Columbus, Ohio USA. In addition, we investigated the dissemination of these CPE into the environment and the downstream watershed, including sediment, fish, mammals, waterfowl, crops and soils. CPE were recovered from each (100 %) of the 44 influent samples and from 37 (84 %) effluent samples. We also isolated CPE from 50 % (22/44) of the upstream water, 82 % (36/44) of downstream, and 68 % (30/44) way downstream water. CPE were most commonly Enterobacter spp. expressing the blaKPC-2 genotype, although a variety of other species and genotypes were observed. blaKPC concentration was greatest in the influent (mean = 106 gene copies/100 mL water) and treatment resulted in a 4-log reduction in blaKPC concentration (P < 0.05), which was consistent with reduction in total bacteria concentration. We found 22 of 450 fish vent swabs (4.9 %) carrying CPE, but CPE were not recovered from terrestrial wildlife living in the Scioto watershed. Fish intestinal microbiome maintained approximately 1.5 × 104 copies of blaKPC per gram of feces. Our data support the hypothesized flow of CPE from healthcare settings into surface water and the downstream natural environment via municipal wastewater discharge. Our results suggest that river environments can serve as a reservoir for CPE, facilitating their broader One Health dissemination among surface water, wildlife, agriculture, and ultimately back to humans.

In vitro human gastrointestinal digestibility and colonic fermentation of edible yeast-based protein: A comparative study with whey and casein

The global protein demand is in constant increase requiring sustainable and healthier alternative proteins for animal and human nutrition. Yeast-based proteins (YBP) represent a non-negligible environmental-friendly fermentation-based solutions with high nutritional quality and bioavailability. Although in vitro studies cannot reflect the full complexity of in vivo digestion, it is considered as useful alternatives to animal models assessing protein digestibility. A 5 h TIM-1 digestion model (TNO Gastro-Intestinal Model) was used to assess the digestibility profile and amino acid bio-accessibility of YBP (3 separate production batches) versus whey and casein as references. Every hour, dialysate and ileal effluent samples were collected. Total nitrogen and free amino acid (FAA) were quantified. To assess the microbial impact, YBP digestate was subjected to 48 h Colon-on-a-Plate batch fermentation, after which the microbial composition by shotgun sequencing and microbial activity by Short-Chain Fatty Acids (SCFAs), Branched-Chain Fatty Acids (BCFAs) (GC-MS) and untargeted metabolomics (LA-REIMS) was analysed (from N = 11 healthy donors of faecal material). YBP, casein and whey were comparable in terms of digestibility. Although YBP showed a different metabolomic fingerprint compared to casein and whey, the microbial activity through SCFA quantification was significantly increased for all proteins compared to blank but not between protein sources. Whey and casein resulted in a higher abundance of Clostridium compared to YBP, while the treatment with YBP resulted in higher abundance of Bacteroides. Altogether, our results suggest that YBP could be a nutritionally relevant alternative protein.

Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance

Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.

Experience and Perspectives on Antibacterial Therapy for Listeriosis in a Tertiary Teaching Hospital in China: A Retrospective Study and Health Care Provider Survey

Listeriosis is a rare, life-threatening bacterial infection. Prompt, appropriate antibiotic treatment is essential to save lives. We aimed to investigate antibiotic selection and listeriosis knowledge among health care providers. We first performed a retrospective study on patients with listeriosis who were treated in a hospital in China from January 2013 to March 2023. Patient characteristics and antibiotic selections were recorded. Antibiotics were classified as effective or ineffective based on the efficacy classifications listed in The Sanford Guide to Antimicrobial Therapy (50th edition). We then conducted a questionnaire survey of health care providers to investigate their listeriosis knowledge and practices between April 2023 to May 2023. Fifteen listeriosis patients were identified, with a case fatality rate of 26.7% (4/15). Empirical treatments assessed as effective antibiotics or ineffective antibiotics were given to 33.3% (5/15) and 66.7% (10/15) of the patients, respectively. After Listeria monocytogenes was identified, 40% (6/15) of the patients received an adjustment to their antibiotics, although 50% (3/6) patients still received ineffective antibiotics. The questionnaire survey of 77 participating health care providers showed that 32.9% (24/73) of the clinicians were unaware of the appropriate antibiotics for listeriosis. Most participants (83.1%, 64/77) would read the drug sensitivity report before selecting the antibiotics. The selection of effective antibiotics differed between the infectious diseases department and other departments (p < 0.001), but did not differ between junior title and other titles (p = 0.088). Most patients with listeriosis did not receive appropriate antibiotics, which might have accounted for the high fatality rate, and may have resulted from inadequate listeriosis knowledge. More education and correct reporting of drug sensitivity results are urgently needed.

Bacterial composition and cultural dynamics of microgreens-associated microbiota during selective enrichment for Listeria monocytogenes

Widely regarded as a so-called "superfood," microgreens have become an increasingly significant food crop from both nutritional and agricultural standpoints. However, similar to other produce commodities that are also cultivated using modernized indoor farming methods, there have been mounting concerns over the potential risks of consuming microgreens contaminated by Listeria monocytogenes. To gain insights into the microbial properties of microgreens, this study characterized the bacterial composition of fresh microgreen retail products using amplicon sequencing of 16S rRNA genes. Dominated by Gammaproteobacteria, a total of 36 shared genera were identified as putative constituents of the microgreen core microbiome. By monitoring the dynamics of microgreen-borne bacteria undergoing a Listeria-selective cultural enrichment procedure, it was revealed that, regardless of the presence or absence of L. monocytogenes, off-target bacteria of the Klebsiella and Enterococcus genera were significantly enriched from microgreens by the primary enrichment step, with the secondary enrichment step continuing to promote the expansion of Enterococcus population. While Listeria was generally neither the most-enriched nor the dominant taxon in cultures sampled at different enrichment stages, significant enrichment of Lysinibacillus and Bacillus bacteria was detected in microgreens contaminated with L. monocytogenes, suggesting they could be co-enriched in competition with Listeria.

Risk factors associated with food consumption and food-handling habits for sporadic listeriosis: a case-control study in China from 2013 to 2022

The prevalence of listeriosis in China has been increasing in recent years. Listeriosis primarily spreads through contaminated food. However, the resilient causative organism, Listeria monocytogenes, and its extended incubation period pose challenges in identifying risk factors associated with food consumption and food-handling habits. This study aimed to identify the risk factors associated with food consumption and food-handling habits for listeriosis in China. A matched case-control study (1:1 ratio) was conducted, which enrolled all eligible cases of listeriosis between 1 January 2013 and 31 December 2022 in China. Basic information and possible risk factors associated with food consumption and food-handling habits were collected. Overall, 359 patients were enrolled, including 208 perinatal and 151 non-perinatal cases. Univariate and multivariable logistic analyzes were performed for the perinatal group. For the perinatal and non-perinatal groups, ice cream and Chinese cold dishes were the high-risk foods for listeriosis (odds ratio (OR) 2.09 95% confidence interval (CI): 1.23-3.55; OR 3.17 95% CI: 1.29-7.81), respectively; consumption of leftovers and pet ownership were the high-risk food-handling habits (OR 1.92 95% CI: 1.03-3.59; OR 3.00 95% CI: 1.11-8.11), respectively. In both groups, separation of raw and cooked foods was a protective factor (OR 0.27 95% CI: 0.14-0.51; OR 0.35 95% CI: 0.14-0.89), while refrigerator cleaning reduced the infection risk by 64.94-70.41% only in the perinatal group. The identification of high-risk foods and food-handling habits for listeriosis is important for improving food safety guidelines for vulnerable populations.

Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia

BACKGROUND

Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed "metabolic endotoxemia." We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.

METHODS

Fifty postmenopausal women (mean age 78.8 ± 5.3 years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n = 25 with low VAT area (45.6 ± 12.5 cm2) and n = 25 with high VAT area (177.5 ± 31.3 cm2). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4 mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6 weeks.

RESULTS

Women in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.

CONCLUSIONS

Increased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms. Video Abstract.

Pre-packaged cold-chain ready-to-eat food as a source of sporadic listeriosis in Beijing, China

OBJECTIVES

Using a sporadic case of listeriosis suspected to have been caused by consuming a pre-packaged cold-chain ready-to-eat (RTE) food in Beijing, China in 2021 as an exemplar, this study demonstrated the importance of thoroughly investigating the source of listeriosis up to the production point for mitigating infection risk during routine monitoring of Listeria in food facilities and national surveillance program using whole-genome sequencing (WGS).

METHODS

Epidemiological, laboratory, traceback, and plant investigations were used to identify the source of infection.

RESULTS

WGS showed the isolate from the patient was genetically indistinguishable from that of the implicated food. During a plant investigation, L. monocytogenes was detected in 26% (9/35) of the environmental samples and one of two raw material samples, confirming the source.

CONCLUSION

To our knowledge, this is the first investigation in China linking a case of L. monocytogenes infection to a suspected food and its production environment. This report highlights the risk of L. monocytogenes contamination of RTE food and demonstrates the role of food safety risk monitoring in identifying potential sources of infection. Reinforcing control programs in RTE processing plants, intensified surveillance of microorganisms in food products and targeted health education is required to mitigate the infection risk.

In Vitro Human Gastrointestinal Digestibility and Colonic Fermentation of Wheat Sourdough and Yeast Breads

Bread can vary in textural and nutritional attributes based on differences in the bread making process (e.g., flour type, fermentation agent, fermentation time). Four bread recipes (BRs) made with sourdough preferments (BR1, white flour; BR2, whole grain flour) or regular yeast breads (BR3, white flour; BR4, whole grain flour) were evaluated for texture, digestibility, and their effect on the metabolic activity and composition of the gut microbiota using texture profile analysis (TPA) coupled with in vitro upper gastrointestinal (GIT) digestion and colonic fermentation (Colon-on-a-plate™ model), using fecal samples from eight healthy human donors. TPA revealed significantly higher values for hardness, fracturability, gumminess, and chewiness, and significantly lower values for springiness, cohesiveness, and resilience with whole grain versus white breads (all p < 0.001); values for springiness, cohesiveness, and resilience were significantly higher for sourdough versus yeast bread (p < 0.001). Nutrient composition and bioaccessibility were generally comparable between sourdough and yeast bread with similar flours. Following simulation of upper GIT digestion, all BRs demonstrated good digestibility of minerals, carbohydrates, and proteins. Colonic fermentation revealed changes in gut microbiota composition, significant increases in short-chain fatty acids, and a significant decrease in branched short-chain fatty acids with all BRs versus a blank. Overall, new insights into wheat bread digestibility and colonic fermentation were provided, which are important aspects to fully characterize bread nutritional profile and potential.

Polyphenol-Rich Cranberry Beverage Positively Affected Skin Health, Skin Lipids, Skin Microbiome, Inflammation, and Oxidative Stress in Women in a Randomized Controlled Trial

This study aimed to determine whether a polyphenol-rich cranberry beverage affects skin properties, lipids, and the microbiome in women using a randomized, double-blinded, placebo-controlled, cross-over design. Twenty-two women with Fitzpatrick skin types 2-3 were randomized to drink a cranberry beverage or placebo for six weeks. After a 21-day washout, they consumed the opposite beverage for six weeks. Six weeks of cranberry beverage significantly reduced UVB-induced erythema, improved net elasticity on the face and forearm, smoothness on the face, and gross elasticity on the forearm compared to the placebo. When stratified by age, these effects of the cranberry beverage were primarily observed in women >40 years old. SOD activities were improved after six weeks of cranberry beverage consumption compared to the placebo, while glutathione peroxide and TNF-α were improved compared to baseline. These effects were found to differ by age group. Skin lipid composition was modulated by both the cranberry beverage and the placebo. Cranberry beverages did not change α- or β-diversity but altered the abundance of several skin microbes at the species and strain level. Consumption of a cranberry beverage for six weeks improved specific skin properties and oxidative stress and modulated skin lipids and microbiome compared to placebo.

Growth assessment of Salmonella enterica multi-serovar populations in poultry rinsates with commonly used enrichment and plating media

Isolation of Salmonella from enrichment cultures of food or environmental samples is a complicated process. Numerous factors including fitness in various selective enrichment media, relative starting concentrations in pre-enrichment, and competition among multi-serovar populations and associated natural microflora, come together to determine which serovars are identified from a given sample. A recently developed approach for assessing the relative abundance (RA) of multi-serovar Salmonella populations (CRISPR-SeroSeq or Deep Serotyping, DST) is providing new insight into how these factors impact the serovars observed, especially when different selective enrichment methods are used to identify Salmonella from a primary enrichment sample. To illustrate this, we examined Salmonella-positive poultry pre-enrichment samples through the selective enrichment process in Tetrathionate (TT) and Rappaport Vassiliadis (RVS) broths and assessed recovery of serovars with each medium. We observed the RA of serovars detected post selective enrichment varied depending on the medium used, initial concentration, and competitive fitness factors, all which could result in minority serovars in pre-enrichment becoming dominant serovars post selective enrichment. The data presented provide a greater understanding of culture biases and lays the groundwork for investigations into robust enrichment and plating media combinations for detecting Salmonella serovars of greater concern for human health.

Evaluation of universal preenrichment broth and comparison of rapid molecular methods for the detection of Salmonella from spent sprout irrigation water (SSIW)

Sprouts and spent sprout irrigation water (SSIW) present unique challenges for the development of a Salmonella detection method in food matrices. This study aimed to compare universal preenrichment broth (UPB) and lactose broth (LB) as preenrichment media for cultural and rapid screening methods and to compare their abilities to recover Salmonella in SSIW samples from different sprout varieties (i.e., alfalfa, broccoli, and mung bean sprouts). The associated co-enriched microbiota with different sprout varieties using different preenrichment media were also examined using a quasi-metagenomic approach. The performance of media and detection methods was compared using the relative level of detection (RLOD) value, as recommended by ISO 16140-2:2016. The level of detection (LOD) for Salmonella culture method with UPB was similar to that with LB in low aerobic plate count (APC) background samples (the relative LOD, i.e., RLOD, was nearly 1 after adjusting for the effects of SSIW variety and serovar), but significantly lower than that with LB in high APC background samples (RLOD = 0.32). The LOD for Salmonella with selected rapid methods was comparable to each other (RLOD from 0.97 to 1.50) and to the culture method (RLOD from 0.69 to 1.03), and no significant difference was detected between preenrichment broths in low APC background samples with RLOD values between 0.76 and 1.04. In samples with a high APC background, however, a drastic difference in LOD was observed between methods and between preenrichment broths for each method. The RLOD ranged from 0.03 to 0.32 when UPB was compared to LB as preenrichment broth. The composition and relative abundance (RA) of co-enriched microbiota was affected by multiple factors including food matrices, preenrichment media and Salmonella contamination. Altogether, this study validated UPB as a better preenrichment broth than LB for the detection of Salmonella enterica from SSIW. This study also suggested UPB may also be an optimal preenrichment medium for rapid screening methods when APC level is high. The observation of potential exclusion of Salmonella in preenrichment through the overgrowth of competitive microflora from the quasi-metagenomic study provided novel information that may be used to further optimize preenrichment formulations.

An Alternative Rapid Confirmation Method for Identifying Listeria monocytogenes from a Variety of 125 g Food Samples Within Two Days of a PCR Presumptive Positive

Cultural confirmation following detection of a Listeria monocytogenespresumptive positive can take 3-7 days to finalize; this uncertainty is a point of frustration for food producers needing to make time-sensitive disposition decisions. To address the demand for shortened time-to-results, an alternative L. monocytogenes confirmation method consisting of two components, (i) a secondary screen using a different rapid method, and (ii) concurrent cultural isolation followed by next-day colony identification was evaluated. For the study, four food matrices (hot dogs, peanut butter, frozen vegetables, and multicomponent frozen meals) were inoculated with low levels (0.36-1.39 MPN/125 g) of L. monocytogenes per the AOAC guidelines for a matrix study. Analyses were performed on 125 g test portions and started with a PCR primary screen (Bio-Rad iQ-Check Listeria monocytogenes II). Next, all enriched food samples underwent a secondary screen by bioMérieux's GENE-UP LMO2 Real-Time PCR and VIDAS LMX ELFA along with streaking onto RAPID'L.mono Agar. Presumptive positive L. monocytogenes colonies were identified utilizing a high throughput rapid identification method (Hygiena's BAX System L. monocytogenes Real-Time PCR assay, Neogen's ANSR isothermal nucleic acid amplification assay, and Bruker's MALDI Biotyper). Importantly, this study evaluated multiple commercially available options for the secondary screen (n = 2) and rapid identification (n = 3) to allow for easy adoption by testing laboratories. Overall, there was no statistically significant difference (p ≤ 0.05) between the number of L. monocytogenes-positive 125 g samples obtained by the cultural reference method and the alternative confirmation methods (regardless of which method combinations were evaluated). Additionally, this study supports that, when both the primary and secondary screen methods yield a positive result, the sample could be considered a confirmed positive for L. monocytogenes.

First insight into the natural biodegradation of cyanide in a gold tailings environment enriched in cyanide compounds

The disposal of mining wastes that contain cyanide are dumped in tailings from gold extraction is a public concern in mining countries such as South Africa. Many studies have shown the potential of microorganisms to degrade cyanide. However, no in-situ exploration, in tailings contaminated with cyanide, of the capability of indigenous microorganisms to act as a natural barrier for cyanide attenuation has been performed. Here we aim to combine geochemical and metagenomics techniques to reveal the genomic machinery of indigenous bacteria to degrade cyanide in gold tailings. Indigenous bacteria (i.e., Alicyclobacillus, Sulfobacillus, Acinetobacter, Achromobacter, and among others) pose the genomic machinery to trigger hydrolytic cyanide degradation using enzymes such as nitrilase, nitrile hydratase (Nhase) and thiocyanate. It seems that the lack of nitrogen sources induces the use of cyanide, which would contribute to its natural attenuation in the gold tailings. Therefore, the bacteria identified could represent the first barrier for the detoxification and degradation of cyanide in the outermost layer of the tailings.

Prospective Randomized, Double-Blind, Placebo-Controlled Study of a Standardized Oral Pomegranate Extract on the Gut Microbiome and Short-Chain Fatty Acids

Punica granatum L., commonly known as the pomegranate, is an abundant source of polyphenols, including hydrolyzable ellagitannins, ellagic acid, anthocyanins, and other bioactive phytochemicals shown to be effective in defending against oxidative stress, and has immunomodulatory activities. Ellagitannins, and their hydrolyzed product ellagic acid, interact with the gut microbiota to yield secondary metabolites known as urolithins that may have health benefits. The objective of this study was to determine the effects of supplementation with a standardized punicalagin-enriched pomegranate extract, Pomella® (250 mg), on the gut microbiome, circulating short-chain fatty acids, and gut microbial-derived ellagitannin metabolite urolithins. A randomized, double-blind, placebo-controlled study was conducted over 4 weeks on healthy volunteers aged 25-55 years. Subjects were randomly assigned to receive either an oral supplement containing 75 mg of punicalagin or an oral placebo. Stool sample collection and venipuncture were performed to analyze the gut microbiome, SCFAs, and urolithin. There was no significant change in the gut microbial diversity in both cohorts after 4 weeks of intervention, but there was a significantly increased relative abundance of Coprococcus eutectus, Roseburia faecis, Roseburia inullnivorans, Ruminococcus bicirculans, Ruminococcus calidus, and Faecalibacterium prausnitzii. Pomegranate extract (PE) supplementation led to the augmentation of circulating propionate levels (p = 0.02) and an increasing trend for acetate levels (p = 0.12). The pomegranate extract (PE) supplementation group had an increased level of circulating urolithins compared to the placebo group (6.6% vs. 1.1%, p = 0.13). PE supplementation correlated with shifts in the gut microbiome and with higher circulating levels of propionate and acetate. Further studies should explore the implications in larger cohorts and over a longer duration.

Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

IMPORTANCE

In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as L. monocytogenes, and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of Listeria culture enrichments of environmental swabs collected from dairy and seafood production facilities. We demonstrated that single-nucleotide polymorphism (SNP) analyses of L. monocytogenes metagenome-assembled genomes (MAGs) from quasimetagenomic data sets can achieve similar resolution as culture isolate whole-genome sequencing. To further understand the impact of genome coverage on MAG SNP cluster resolution, an in silico downsampling approach was employed to reduce the percentage of target pathogen sequence reads, providing an initial estimate of required MAG coverage for subtyping resolution of L. monocytogenes.

Systematic Review and Meta-Analysis of Campylobacter Species Contamination in Poultry, Meat, and Processing Environments in South Korea

Campylobacter spp. constitute a significant global threat as a leading cause of foodborne illnesses, with poultry meat as a prominent reservoir for these pathogens. South Korea is known for its diverse poultry consumption habits, and continuous outbreaks make it a matter of concern to perform a meta-analysis to identify the primary source of contamination. This systematic review and meta-analysis aimed to assess and compare the prevalence of Campylobacter in various poultry and meat types while also considering the importance of environmental factors in South Korea. The meta-analysis revealed that duck meat exhibited the highest prevalence of Campylobacter, with a pooled estimate of 70.46% (95% CI: 42.80% to 88.38%), followed by chicken meat at a pooled prevalence of 36.17% (95% CI: 26.44% to 47.91%). Additionally, our analysis highlighted the predominance of C. jejuni and C. coli in South Korea. These findings underscore the importance of implementing rigorous food safety measures and establishing robust surveillance programs in the poultry industry to mitigate the risk of Campylobacter-related foodborne illnesses associated with meat consumption in South Korea.

Ex Vivo Colonic Fermentation of NUTRIOSE® Exerts Immuno-Modulatory Properties and Strong Anti-Inflammatory Effects

NUTRIOSE® (Roquette, Lestrem, France) is a resistant dextrin with well-established prebiotic effects. This study evaluated the indirect effects of pre-digested NUTRIOSE® on host immune response and gut barrier integrity. Fecal samples from eight healthy donors were inoculated in a Colon-on-a-plate® system (ProDigest, Ghent, Belgium) with or without NUTRIOSE® supplementation. Following 48 h fermentation, colonic suspensions were tested in a Caco-2/THP1-Blue™ co-culture system to determine their effects on gut barrier activity (transepithelial electrical resistance) and immune response following lipopolysaccharide stimulation. Additionally, changes in short-chain fatty acid levels (SCFA) and microbial community composition following a 48 h fermentation in the Colon-on-a-plate® system were measured. Across all donors, immune-mediated intestinal barrier damage was significantly reduced with NUTRIOSE®-supplemented colonic suspensions versus blank. Additionally, IL-6 and IL-10 levels were significantly increased, and the level of the neutrophil chemoattractant IL-8 was significantly decreased with NUTRIOSE®-supplemented colonic suspensions versus blank in the co-culture models following lipopolysaccharide stimulation. These beneficial effects of NUTRIOSE® supplementation were likely due to increased acetate and propionate levels and the enrichment of SCFA-producing bacteria. NUTRIOSE® was well fermented by the colonic bacteria of all eight donors and had protective effects on inflammation-induced disruption of the intestinal epithelial barrier and strong anti-inflammatory effects.

Correlating the Gut Microbiota and Circulating Hormones with Acne Lesion Counts and Skin Biophysical Features

Acne vulgaris is a common inflammatory condition that is multi-factorial and impacted by both intrinsic and extrinsic features. Several previous studies have assessed for correlations between factors such as circulating hormones, stress, or the microbiome. However, there have not been any correlations specifically against lesion counts or differentiating correlations between inflammatory and non-inflammatory lesion counts. Here, we correlate several factors against acne lesions. Twenty men and women with mild to moderate acne were recruited, and their hormonal levels and their gut microbiome were collected and correlated against their inflammatory and non-inflammatory lesions of acne. Facial non-inflammatory lesions were weakly correlated to sebum excretion rate and weakly inversely correlated to forehead and cheek hydration. We examined stress through the use of a normalized peak-to-trough ratio (higher numbers indicated less stress), which correlated with skin hydration and inversely correlated with sebum excretion rate. Sebum excretion rate was weakly correlated to testosterone levels, and facial hydration correlated with estradiol levels. Correlations with the gut microbiome showed differential correlations with inflammatory and non-inflammatory lesions, with Clostridium sp AF 23-8 correlating to inflammatory lesion counts, while Actinomyces naeslundii str Howell 279 correlated to non-inflammatory lesions. Overall, measures of stress and circulating hormones correlate to skin biophysical properties and acne lesion counts. Also, different gut bacteria correlate with either inflammatory or non-inflammatory lesion counts. We hope that our findings stimulate further work on the gut-mind-stress-skin axis within acne.

bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting

Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, we introduce bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal is one of the first analysis tools to identify multiple Salmonella enterica serotypes from metagenomic or quasi-metagenomic datasets with high accuracy, allowing these isolate-independent methods to be incorporated into surveillance and root cause investigations. It was tested on an in silico benchmark dataset comprising 29 unique Salmonella serovars, 46 non-Salmonella bacterial genomes, and 10 viral genomes at varying read depths and on previously well-characterized and sequenced non-selective primary and selective enrichments of papaya and peach samples from separate outbreak investigations that resulted in the identification of multiple Salmonella serovars using traditional isolate culturing and WGS as well as nucleic acid assays. Analyses were also conducted on these datasets using a custom-built k-mer tool, SeqSero2, and Kallisto to compare serotype calling to bettercallsal. The in silico dataset analyzed with bettercallsal achieved the maximum precision, recall, and accuracy of 100, 83, and 94%, respectively. In the papaya outbreak samples, bettercallsal identified the presence of multiple serovars in agreement with the Luminex® xMAP assay results and also identified more serovars per sample, as evidenced by NCBI SNP clustering. In peach outbreak samples, bettercallsal identified two serovars in concordance with k-mer analysis and the Luminex xMAP assay. The genome hit reported by bettercallsal clustered with the chicken isolate genome, as reported by the FDA peach outbreak investigation from sequenced isolates (WGS). Overall, bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.

Antimicrobial Susceptibility Profile of Listeria monocytogenes Isolated from Meat Products: A Systematic Review and Meta-Analysis

The objective of this study was to conduct a systematic review to comprehensively understand antimicrobial resistance (AMR) in Listeria monocytogenes (LM) isolated from meat and meat products. The study was performed following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Published articles from 2000 to 2022 were collected from six widely used online databases, including AGRICOLA, PubMed, Web of Science (WoS), Scopus, Cochrane Library, and CINAHL-EBSCO. Prevalence rates and AMR of pathogen isolates were analyzed using MedCalc software, including the I2 statistic and Cochrane Q test for heterogeneity. Sensitivity analysis, subgroup analysis, and meta-regression were conducted to analyze potential sources of heterogeneity at a 95% significance level. The distribution and prevalence of multidrug resistance (MDR) were examined using a random-effect model. The pooled frequency of bacterial MDR was 22.97% (95% confidence interval [CI] = 14.95-32.13). The studies exhibited high heterogeneity (I2 = 94.82%, 95% CI = 93.74-95.71, p < 0.0001). Furthermore, the most prevalent antibiotics resistance found in the majority of included studies were tetracycline, clindamycin, penicillin, ampicillin, and oxacillin (I2 = 86.66%, 95% CI = 73.20-93.36, p < 0.0001). This meta-analysis provides a comprehensive understanding of AMR in LM isolates, and the results indicate that none of the variable factors, including sampling location, sampling size, or methodology, significantly influenced the outcome of LM isolates resistant to multidrug.

Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach

BACKGROUND

The reliability of culture-independent pathogen detection in foods using metagenomics is contingent on the quality and composition of the reference database. The inclusion of microbial sequences from a diverse representation of taxonomies in universal reference databases is recommended to maximize classification precision for pathogen detection. However, these sizable databases have high memory requirements that may be out of reach for some users. In this study, we aimed to assess the performance of a foodborne pathogen (FBP)-specific reference database (taxon-specific) relative to a universal reference database (taxon-agnostic). We tested our FBP-specific reference database's performance for detecting Listeria monocytogenes in two complex food matrices-ready-to-eat (RTE) turkey deli meat and prepackaged spinach-using three popular read-based DNA-to-DNA metagenomic classifiers: Centrifuge, Kraken 2 and KrakenUniq.

RESULTS

In silico host sequence removal led to substantially fewer false positive (FP) classifications and higher classification precision in RTE turkey deli meat datasets using the FBP-specific reference database. No considerable improvement in classification precision was observed following host filtering for prepackaged spinach datasets and was likely a consequence of a higher microbe-to-host sequence ratio. All datasets classified with Centrifuge using the FBP-specific reference database had the lowest classification precision compared to Kraken 2 or KrakenUniq. When a confidence-scoring threshold was applied, a nearly equivalent precision to the universal reference database was achieved for Kraken 2 and KrakenUniq. Recall was high for both reference databases across all datasets and classifiers. Substantially fewer computational resources were required for metagenomics-based detection of L. monocytogenes using the FBP-specific reference database, especially when combined with Kraken 2.

CONCLUSIONS

A universal (taxon-agnostic) reference database is not essential for accurate and reliable metagenomics-based pathogen detection of L. monocytogenes in complex food matrices. Equivalent classification performance can be achieved using a taxon-specific reference database when the appropriate quality control measures, classification software, and analysis parameters are applied. This approach is less computationally demanding and more attainable for the broader scientific and food safety communities.

Shared and Distinct Gut Microbial Profiles in Saudi Women with Metabolically Healthy and Unhealthy Obesity

BACKGROUND

Mounting evidence suggests a pivotal role for the gut microbiome in energy disequilibrium characteristic of obesity. The clinical utility of microbial profiling for the distinction between metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO) remains ill-defined. We aim to probe microbial composition and diversity in young adult Saudi females with MHO and MUO. This observational study included anthropometric and biochemical measurements and shotgun sequencing of stool DNA for 92 subjects. α- and β-diversity metrics were calculated to determine the richness and variability in microbial communities, respectively. Results showed that Bacteroides and Bifidobacterium merycicum were less abundant in MUO compared to healthy and MHO groups. BMI was negatively correlated with B. adolescentis, B. longum, and Actinobacteria in MHO, while being positively correlated with Bacteroides thetaiotaomicron in both MHO and MUO. Positive correlations between waist circumference and B. merycicum and B. thetaiotaomicron were observed in MHO and MUO, respectively. Compared to MHO and MUO groups, higher α-diversity was detected in healthy individuals who also had higher β-diversity compared to those with MHO. We conclude that modulation of the gut microbiome cohorts through prebiotics, probiotics, and fecal microbiota transplantation may be a promising preventive and therapeutic approach to obesity-associated disease.

An Overview of Foodborne Sample-Initiated Retrospective Outbreak Investigations and Interagency Collaboration in the United States

Foodborne outbreak investigations have traditionally included the detection of a cluster of illnesses first, followed by an epidemiologic investigation to identify a food of interest. The increasing use of whole genome sequencing (WGS) subtyping technology for clinical, environmental, and food isolates of foodborne pathogens, and the ability to share and compare the data on public platforms, present new opportunities to identify earlier links between illnesses and their potential sources. We describe a process called sample-initiated retrospective outbreak investigations (SIROI) used by federal public health and regulatory partners in the United States. SIROIs begin with an evaluation of the genomic similarity between bacterial isolates recovered from food or environmental samples and clusters of clinical isolates while subsequent and parallel epidemiologic and traceback investigations are initiated to corroborate their connection. SIROIs allow for earlier hypothesis generation, followed by targeted collection of information about food exposures and the foods and manufacturer of interest, to confirm a link between the illnesses and their source. This often leads to earlier action that could reduce the breadth and burden of foodborne illness outbreaks. We describe two case studies of recent SIROIs and present the benefits and challenges. Benefits include insight into foodborne illness attribution, international collaboration, and opportunities for enhanced food safety efforts in the food industry. Challenges include resource intensiveness, variability of epidemiologic and traceback data, and an increasingly complex food supply chain. SIROIs are valuable in identifying connections among small numbers of illnesses that may span significant time periods; detecting early signals for larger outbreaks or food safety issues associated with manufacturers; improving our understanding of the scope of contamination of foods; and identifying novel pathogen/commodity pairs.

Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women

(1) Background: Gut microbiota dysbiosis may lead to diseases such as insulin resistance and obesity. We aimed to investigate the relationship between insulin resistance, body fat distribution, and gut microbiota composition. (2) Methods: The present study included 92 Saudi women (18–25 years) with obesity (body mass index (BMI) ≥ 30 kg/m2, n = 44) and with normal weight (BMI 18.50–24.99 kg/m2, n = 48). Body composition indices, biochemical data, and stool samples were collected. The whole-genome shotgun sequencing technique was used to analyze the gut microbiota. Participants were divided into subgroups stratified by the homeostatic model assessment for insulin resistance (HOMA-IR) and other adiposity indices. (3) Results: HOMA-IR was inversely correlated with Actinobacteria (r = −0.31, p = 0.003), fasting blood glucose was inversely correlated with Bifidobacterium kashiwanohense (r = −0.22, p = 0.03), and insulin was inversely correlated with Bifidobacterium adolescentis (r = −0.22, p = 0.04). There were significant differences in α- and β-diversities in those with high HOMA-IR and waist–hip ratio (WHR) compared to low HOMA-IR and WHR (p = 0.02, 0.03, respectively). (4) Conclusions: Our findings highlight the relationship between specific gut microbiota at different taxonomic levels and measures of glycemic control in Saudi Arabian women. Future studies are required to determine the role of the identified strains in the development of insulin resistance.

Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses

The intestinal immune system interacts with commensal microbiota to maintain gut homeostasis. Furthermore, stress alters the microbiome composition, leading to impaired brain function; yet how the intestinal immune system mediates these effects remains elusive. Here we report that colonic γδ T cells modulate behavioral vulnerability to chronic social stress via dectin-1 signaling. We show that reduction in specific Lactobacillus species, which are involved in T cell differentiation to protect the host immune system, contributes to stress-induced social-avoidance behavior, consistent with our observations in patients with depression. Stress-susceptible behaviors derive from increased differentiation in colonic interleukin (IL)-17-producing γδ T cells (γδ17 T cells) and their meningeal accumulation. These stress-susceptible cellular and behavioral phenotypes are causally mediated by dectin-1, an innate immune receptor expressed in γδ T cells. Our results highlight the previously unrecognized role of intestinal γδ17 T cells in the modulation of psychological stress responses and the importance of dectin-1 as a potential therapeutic target for the treatment of stress-induced behaviors.

Gut virome profile in healthy Saudi children

Background

The role of viruses is well known in health and disease. The aim of this report was to describe the profile of viruses in the gut of healthy Saudi children.

Methods

In 20 randomly selected school age children from Riyadh, stool samples were collected in cryovials and stored at -80° C. At the time of analysis, the samples were sent by express mail in a temperature-controlled container to the laboratory in the USA, Viral DNA was isolated and shotgun metagenomic sequencing was performed. The abundance of each organism was expressed as an average relative percentage across the viral phylogenetic tree from phyla to species.

Results

The median age of the children was 11.3 (range 6.8-15.4) years, and 35% were males. Caudovirales were the most abundant bacteriophage order (77%) and Siphoviridae, Myoviridae, and Podoviridae families predominated, accounting for 41%, 25%, and 11%, respectively. Among the viral bacteriophage species, the most abundant were the Enterobacteria phages.

Conclusion

The profile and abundance of the gut virome in healthy Saudi children reveal important differences from the literature. Further studies from different populations with larger sample sizes are needed to understand the role of gut viruses in the pathogenesis of disease in general and in the response to fecal microbiota therapy in particular.

Galactooligosaccharide (GOS) Reduces Branched Short-Chain Fatty Acids, Ammonium, and pH in a Short-Term Colonic Fermentation Model

Prebiotics beneficially affect the gut microbiome. Bimuno®, a prebiotic supplement containing galactooligosaccharides (GOS), has multiple demonstrated prebiotic effects. Using short-term colonic incubations, the influence of GOS on the colonic microbiota of three healthy human adults was evaluated. Colonic reactors inoculated with fecal samples were untreated (blank) or supplemented with GOS. pH, gas pressure, short-chain fatty acids (SCFAs), lactic acid, branched SCFAs, ammonium, and microbial community composition were evaluated at 0 h, 6 h, 24 h, and 48 h. pH decreased and gas pressure increased (+29.01 kPa) with GOS treatment versus blank. Total SCFA (+22.4 mM), acetate (+14.1 mM), propionate (+5.5 mM), and butyrate (+5.8 mM) were higher for GOS than blank. Acetate and propionate production were highest earlier in the experiment, while butyrate production was highest between 24 h and 48 h. With GOS, lactic acid production increased between 0 h and 6 h (+14.4 mM) followed by apparent consumption. Levels of branched SCFAs and ammonium were low with GOS and reduced versus blank (respectively, −2.1 mM and −256.0 mg/L). GOS significantly increased the relative abundance of Bifidobacterium longum (LDA = 4; p = 0.006), and significantly increased the absolute abundance of Bifidobacteriaceae (p < 0.001), Lactobacillaceae (p < 0.05), Bifidobacterium adolescentis (LDA = 4.5; p < 0.001), and Bifidobacterium ruminantium (LDA= 3.2; p = 0.01). This in vitro model demonstrated the prebiotic potential of GOS as supplementation resulted in increased beneficial bacteria, SCFA, and lactic acid and decreased branched SCFA, pH, and ammonium.

Malaria disrupts the rhesus macaque gut microbiome

Previous studies have suggested that a relationship exists between severity and transmissibility of malaria and variations in the gut microbiome, yet only limited information exists on the temporal dynamics of the gut microbial community during a malarial infection. Here, using a rhesus macaque model of relapsing malaria, we investigate how malaria affects the gut microbiome. In this study, we performed 16S sequencing on DNA isolated from rectal swabs of rhesus macaques over the course of an experimental malarial infection with Plasmodium cynomolgi and analyzed gut bacterial taxa abundance across primary and relapsing infections. We also performed metabolomics on blood plasma from the animals at the same timepoints and investigated changes in metabolic pathways over time. Members of Proteobacteria (family Helicobacteraceae) increased dramatically in relative abundance in the animal's gut microbiome during peak infection while Firmicutes (family Lactobacillaceae and Ruminococcaceae), Bacteroidetes (family Prevotellaceae) and Spirochaetes amongst others decreased compared to baseline levels. Alpha diversity metrics indicated decreased microbiome diversity at the peak of parasitemia, followed by restoration of diversity post-treatment. Comparison with healthy subjects suggested that the rectal microbiome during acute malaria is enriched with commensal bacteria typically found in the healthy animal's mucosa. Significant changes in the tryptophan-kynurenine immunomodulatory pathway were detected at peak infection with P. cynomolgi, a finding that has been described previously in the context of P. vivax infections in humans. During relapses, which have been shown to be associated with less inflammation and clinical severity, we observed minimal disruption to the gut microbiome, despite parasites being present. Altogether, these data suggest that the metabolic shift occurring during acute infection is associated with a concomitant shift in the gut microbiome, which is reversed post-treatment.

Red and White Meat Intake in Relation to Gut Flora in Obese and Non-Obese Arab Females

BACKGROUND

high meat intake may contribute to several chronic diseases including obesity. However, evidence is insufficient on the relation between red/white meat intake and gut flora among individuals with varying degrees of adiposity.

OBJECTIVE

investigate the association of red/white meat intake with gut flora in Saudi Arabian females with/without obesity.

METHODS

this observational study involved 92 females with and without obesity (n = 44, 48, respectively) aged 19-25 years. The whole-genome shotgun technique was used to analyze the gut flora. Shannon alpha and Bray-Curtis beta diversity as well as correlation coefficients were used.

RESULTS

in the total sample, there were positive correlations between Actinobacteria, Bacteroides (p ≤ 0.05), Flavonifractor plautii (p ≤ 0.0001), and total red meat intake. There were also positive correlations between total white meat intake, Bacteroides, and Faecalibacterium prausnitzii (p ≤ 0.05) in the total sample. In the group without obesity, there was a positive correlation between low white meat intake and Actinobacteria (p = 0.05). In the group with obesity, there was a positive correlation between high white meat intake and Bacteroides (p ≤ 0.001).

CONCLUSION

our findings suggest that meat intake had an impact on the gut flora of Arab adult females, independent of adiposity. Specific strains identified in this study need further investigation to determine their relation to meat intake and obesity.

Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: a network theory approach

The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, the molecular mechanisms involved in such therapies are often not well understood, particularly when targeting the small intestinal microbiota. In this study, we investigated the effects of a probiotic formula (Ecologic®825) on the adult human small intestinal ileostoma microbiota. The results showed that supplementation with the probiotic formula led to a reduction in the growth of pathobionts, such as Enterococcaceae and Enterobacteriaceae, and a decrease in ethanol production. These changes were associated with significant alterations in nutrient utilization and resistance to perturbations. These probiotic mediated alterations which coincided with an initial increase in lactate production and decrease in pH were followed by a sharp increase in the levels of butyrate and propionate. Moreover, the probiotic formula increased the production of multiple N-acyl amino acids in the stoma samples. The study demonstrates the utility of network theory in identifying novel microbiota-targeted therapies and improving existing ones. Overall, the findings provide insights into the dynamic molecular mechanisms underlying probiotic therapies, which can aid in the development of more effective treatments for a range of conditions.

Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar

Microbial rewilding, whereby exposure to naturalistic environments can modulate or augment gut microbiomes and improve host-microbe symbiosis, is being harnessed as an innovative approach to human health, one that may also have significant value to animal care and conservation. To test for microbial rewilding in animal microbiomes, we used a unique population of wild-born ring-tailed lemurs (Lemur catta) that were initially held as illegal pets in unnatural settings and, subsequently, relocated to a rescue center in Madagascar where they live in naturalistic environments. Using amplicon and shotgun metagenomic sequencing of lemur and environmental microbiomes, we found multiple lines of evidence for microbial rewilding in lemurs that were transitioned from unnatural to naturalistic environments: A lemur's duration of exposure to naturalistic settings significantly correlated with (a) increased compositional similarly to the gut communities of wild lemurs, (b) decreased proportions of antibiotic resistance genes that were likely acquired via human contact during pethood, and (c) greater covariation with soil microbiomes from natural habitats. Beyond the inherent psychosocial value of naturalistic environments, we find that actions, such as providing appropriate diets, minimizing contact with humans, and increasing exposure to natural environmental consortia, may assist in maximizing host-microbe symbiosis in animals under human care.

Gut microbial dysbiosis correlates with stroke severity markers in aged rats

Background

An imbalanced gut microbial community, or dysbiosis, has been shown to occur following stroke. It is possible that this dysbiosis negatively impacts stroke recovery and rehabilitation. Species level resolution measurements of the gut microbiome following stroke are needed to develop and test precision interventions such as probiotic or fecal microbiota transplant therapies that target the gut microbiome. Previous studies have used 16S rRNA amplicon sequencing in young male mice to obtain broad profiling of the gut microbiome at the genus level following stroke, but further investigations will be needed with whole genome shotgun sequencing in aged rats of both sexes to obtain species level resolution in a model which will better translate to the demographics of human stroke patients.

Methods

Thirty-nine aged male and female rats underwent middle cerebral artery occlusion. Fecal samples were collected before stroke and 3 days post stroke to measure gut microbiome. Machine learning was used to identify the top ranked bacteria which were changed following stroke. MRI imaging was used to obtain infarct and edema size and cerebral blood flow (CBF). ELISA was used to obtain inflammatory markers.

Results

Dysbiosis was demonstrated by an increase in pathogenic bacteria such as Butyricimonas virosa (15.52 fold change, p < 0.0001), Bacteroides vulgatus (7.36 fold change, p < 0.0001), and Escherichia coli (47.67 fold change, p < 0.0001). These bacteria were positively associated with infarct and edema size and with the inflammatory markers Ccl19, Ccl24, IL17a, IL3, and complement C5; they were negatively correlated with CBF. Conversely, beneficial bacteria such as Ruminococcus flavefaciens (0.14 fold change, p < 0.0001), Akkermansia muciniphila (0.78 fold change, p < 0.0001), and Lactobacillus murinus (0.40 fold change, p < 0.0001) were decreased following stroke and associated with all the previous parameters in the opposite direction of the pathogenic species. There were not significant microbiome differences between the sexes.

Conclusion

The species level resolution measurements found here can be used as a foundation to develop and test precision interventions targeting the gut microbiome following stroke. Probiotics that include Ruminococcus flavefaciens, Akkermansia muciniphila, and Lactobacillus murinus should be developed to target the deficit following stroke to measure the impact on stroke severity.

Prospective Randomized Double-Blind Placebo-Controlled Study of Oral Pomegranate Extract on Skin Wrinkles, Biophysical Features, and the Gut-Skin Axis

(1) Background: The pomegranate fruit (Punica granatum L.) has been widely used in traditional medicine and has increasingly gained popularity among consumers in order to manage different facets of health. The objective of this study was to evaluate the effects of the fruit extract of P. granatum L. on different parameters of skin health. (2) Methods: A prospective, double-blind placebo-controlled study was conducted on both healthy males and females aged 25−55 years. Subjects were supplemented with a standardized punicalagin enriched oral pomegranate extract [Pomella® (Verdure Science, Noblesville, IN, USA), PE group] or a placebo (control group) daily for four weeks. Changes in wrinkle severity, facial biophysical properties, skin microbiome, and the gut microbiome were assessed. (3) Results: The PE group had significant reductions in wrinkle severity (p < 0.01) and a decreasing trend in the forehead sebum excretion rate (p = 0.14). The participants in the PE group with a higher relative abundance of Eggerthellaceae in the gut had a decrease in their facial TEWL (p < 0.05) and wrinkle severity (p = 0.058). PE supplementation led to an increase in the Staphylococcus epidermidis species and the Bacillus genus on the skin. (4) Conclusions: Overall, the study demonstrated improvements in several biophysical properties, wrinkles, and shifts in the skin microbiome with oral PE supplementation in healthy subjects.

Occurrence of Listeria spp. in Soft Cheese and Ice Cream: Effect of Probiotic Bifidobacterium spp. on Survival of Listeria monocytogenes in Soft Cheese

Listeria monocytogenes is one of the most important emerging foodborne pathogens. The objectives of this work were to investigate the incidence of Listeria spp. and L. monocytogenes in soft cheese and ice cream in Assiut city, Egypt, and to examine the effect of some probiotic Bifidobacterium spp. (Bifidobacterium breve, Bifidobacterium animalis, or a mixture of the two) on the viability of L. monocytogenes in soft cheese. The existence of Listeria spp. and L. monocytogenes was examined in 30 samples of soft cheese and 30 samples of ice cream. Bacteriological analyses and molecular identification (using 16S rRNA gene and hlyA gene for Listeria spp. and L. monocytogenes, respectively) were performed on those samples. Additionally, Bifidobacterium spp. were incorporated in the making of soft cheese to study their inhibitory impacts on L. monocytogenes. Out of 60 samples of soft cheese and ice cream, 25 samples showed Listeria spp., while L. monocytogenes was found in only 2 soft cheese samples. Approximately 37% of soft cheese samples (11 out of 30) had Listeria spp. with about 18.0% (2 out of 11) exhibiting L. monocytogenes. In ice cream samples, Listeria spp. was presented by 47% (14 out of 30), while L. monocytogenes was not exhibited. Moreover, the addition of B. animalis to soft cheese in a concentration of 5% or combined with B. breve with a concentration of 2.5% for each resulted in decreasing L. monocytogenes efficiently during the ripening of soft cheese for 28 d. Listeria spp. is widely found in milk products. Probiotic bacteria, such as Bifidobacterium spp., can be utilized as a natural antimicrobial to preserve food and dairy products.

Effects of combined prebiotic, probiotic, IgG and amino acid supplementation on the gut microbiome of patients with inflammatory bowel disease

Background: The effects of the Total Gut Restoration (TGR) system supplementation on the gut microbiome were evaluated. Materials & methods: A mucosal in vitro simulation of the human gastrointestinal tract (M-SHIME®) system was inoculated with fecal samples from patients with inflammatory bowel disease. Chambers were supplemented for 5 days with the TGR system (five probiotic Bacillus strains, prebiotic mixture, immunoglobulin concentrate, amino acids and prebiotic flavonoids). Results: Compared with unsupplemented controls, supplementation was associated with a significant increase in short-chain fatty acid production, and changes to the microbiome were observed. Supernatants from supplemented chambers improved intestinal barrier function, increased IL-6 and IL-10 production and decreased MCP1 production versus control in Caco-2/THP1 coculture. Conclusion: Daily TGR supplementation facilitated changes to the gut microbiome of patients with inflammatory bowel disease.

Oral ingestion of the environmental toxicant trichloroethylene in rats induces alterations in the gut microbiome: Relevance to idiopathic Parkinson's disease

Microbial alterations within the gut microbiome appear to be a common feature of individuals with Parkinson's disease (PD), providing further evidence for the role of the gut-brain axis in PD development. As a major site of contact with the environment, questions have emerged surrounding the cause and effect of alterations to the gut microbiome by environmental contaminants associated with PD risk, such as pesticides, metals, and organic solvents. Recent data from our lab shows that ingestion of the industrial byproduct and environmental pollutant trichloroethylene (TCE) induces key Parkinsonian pathology within aged rats, including the degeneration of dopaminergic neurons, α-synuclein accumulation, neuroinflammation, and endolysosomal deficits. As TCE is the most common organic contaminant within drinking water, we postulated that ingestion of TCE associated with PD-related neurodegeneration may alter the gut microbiome to a similar extent as observed in persons with PD. To assess this, we collected fecal samples from adult rats treated with 200 mg/kg TCE over 6 weeks via oral gavage - the dose that produced nigrostriatal neurodegeneration - and analyzed the gut microbiome via whole genome shotgun sequencing. Our results showed changes in gut microorganisms reflective of the microbial signatures observed in individuals with idiopathic PD, such as decreased abundance of short-chain fatty acid producing Blautia and elevated lactic-acid producing Bifidobacteria, as well as genera who contain species previously reported as opportunistic pathogens such as Clostridium. From these experimental data, we postulate that TCE exposure within contaminated drinking water could induce alterations of the gut microbiome that contributes to chronic disease risk, including idiopathic PD.

Microbiota profile of new-onset celiac disease in children in Saudi Arabia

Background

Intestinal dysbiosis has been reported to be associated with celiac disease (CeD) in Western populations but little is known in other populations who have different dietary lifestyle and genetic background. The purpose of this study was to determine whether a different microbiota profile is associated with CeD in children in Saudi Arabia.

Results

Forty children with CeD, 20 healthy controls, and 19 non-CeD controls were enrolled. The median age at diagnosis was 10.3, 11.3 and 10.6 years in children with CeD, fecal, and mucosal control groups, respectively. Significant differences in microbial composition between children with CeD and controls both at fecal and mucosal level were identified. Fecal samples were more diverse and richer in bacteria as compared with mucosal samples. Proteobacteria were more abundant in duodenal mucosal samples and Firmicutes and Bacteroides were more abundant in stools. The abundance of many taxa was significantly different between children with CeD and non-CeD controls. In mucosal samples, Bifidobacterium angulatum (unadjusted p = 0.006) and Roseburia intestinalis (unadjusted p = 0.031) were examples of most significantly increased species in children with CeD and non-CeD controls, respectively. In fecal samples, there were 169 bacterial species with significantly different abundance between children with CeD and non- CeD controls.

Conclusions

To our knowledge, this is the first report on the microbial profile in a non-Western population of children with new onset CeD. The fact that mucosal and fecal samples were collected from newly diagnosed children with CeD on normal gluten-containing diet suggests strong association between the identified bacteria and CeD. The identification of many unreported bacterial species significantly associated with CeD, indicates the need for further studies from different populations to expand our understanding of the role of bacteria in the pathogenesis of CeD, hopefully leading to the discovery of new adjuvant treatment options.

Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes

Listeria monocytogenes is a leading foodborne pathogen that can contaminate fresh produce in farm environment, resulting in deadly outbreaks. Composts contain a diversity of microorganisms, and some of them may be compost-adapted competitive exclusion microorganisms against L. monocytogenes. To understand interactions between compost microflora and the pathogen, both dairy- and poultry-wastes based composts (n = 12) were inoculated with L. monocytogenes, and then analyzed by next-generation sequencing approaches along with culturing methods. DNA extraction and enumeration of L. monocytogenes were performed at 0 and 72 h post-incubation at room temperature. The major bacterial phyla were identified as Firmicutes (23%), Proteobacteria (23%), Actinobacteria (19%), Chloroflexi (13%), Bacteroidetes (12%), Gemmatimonadetes (2%), and Acidobacteria (2%). The top three indicator genera enriched in different compost types were identified by LEfSe with LDA score > 2. The interactions between L. monocytogenes and indigenous microflora were limited as no significant changes in the dominant microbial members in compost ecosystem, but some discriminatory species such as Bacillus, Geobacillus, and Brevibacterium were identified by Random Forest analysis. Besides, changes in metabolic pathways and the increased abundance of bacteriocins category in the compost samples containing L. monocytogenes after 72 h postinoculation were revealed by metatranscriptomic sequencing. Taken together, the compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbial compositions, and the analysis of compost metagenome implied that interactions between L. monocytogenes and compost microflora may include competition for nutrients and the presence of antimicrobials. IMPORTANCE Listeria monocytogenes has been recognized as the etiological agent causing foodborne disease outbreaks, with fresh produce as vulnerable for contamination at even preharvest stage. Owing to the richness in microbial community, compost may mediate suppression of pathogens. In this study, the impact of compost-related factors and L. monocytogenes intrusion on dynamic changes in compost microbiome was investigated by next generation sequencing techniques. The compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbiome. The interactions between L. monocytogenes and compost microflora may include the competition for nutrients and the presence of antimicrobials produced by native compost microorganisms as potential competitive exclusion microorganisms. Findings from this study are important for the composting industry to understand the composition and functionality of microbial community in their products and help developing organic fertilizers fortified with anti-L. monocytogenes competitive exclusion microorganisms.

Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment

Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments. However, the phylogeny of this genus and its adaptive mechanisms in the geothermal sites of cold environments remain unknown. To the best of our knowledge, this is the first study to unravel the genomic features and provide insights into the phylogenomics and metabolic potential of members of the genus Anoxybacillus inhabiting the Antarctic thermophilic ecosystem. Here, we report the genome sequencing data of seven A. flavithermus strains isolated from two geothermal sites on Deception Island, Antarctic Peninsula. Their genomes were approximately 3.0 Mb in size, had a G + C ratio of 42%, and were predicted to encode 3500 proteins on average. We observed that the strains were phylogenomically closest to each other (Average Nucleotide Identity (ANI) > 98%) and to A. flavithermus (ANI 95%). In silico genomic analysis revealed 15 resistance and metabolic islands, as well as genes related to genome stabilization, DNA repair systems against UV radiation threats, temperature adaptation, heat- and cold-shock proteins (Csps), and resistance to alkaline conditions. Remarkably, glycosyl hydrolase enzyme-encoding genes, secondary metabolites, and prophage sequences were predicted, revealing metabolic and cellular capabilities for potential biotechnological applications.

Skin Injury Activates a Rapid TRPV1-Dependent Antiviral Protein Response

The skin serves as the interface between the body and the environment and plays a fundamental role in innate antimicrobial host immunity. Antiviral proteins (AVPs) are part of the innate host defense system and provide protection against viral pathogens. How breach of the skin barrier influences innate AVP production remains largely unknown. In this study, we characterized the induction and regulation of AVPs after skin injury and identified a key role of TRPV1 in this process. Transcriptional and phenotypic profiling of cutaneous wounds revealed that skin injury induces high levels of AVPs in both mice and humans. Remarkably, pharmacologic and genetic ablation of TRPV1-mediated nociception abrogated the induction of AVPs, including Oas2, Oasl2, and Isg15 after skin injury in mice. Conversely, stimulation of TRPV1 nociceptors was sufficient to induce AVP production involving the CD301b+ cells‒IL-27‒mediated signaling pathway. Using IL-27 receptor‒knockout mice, we show that IL-27 signaling is required in the induction of AVPs after skin injury. Finally, loss of TRPV1 signaling leads to increased viral infectivity of herpes simplex virus. Together, our data indicate that TRPV1 signaling ensures skin antiviral competence on wounding.

Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models

A strong association between exposure to the common harmful algal bloom toxin microcystin and the altered host gut microbiome has been shown. We tested the hypothesis that prior exposure to the cyanotoxin microcystin-LR may alter the host resistome. We show that the mice exposed to microcystin-LR had an altered microbiome signature that harbored antibiotic resistance genes. Host resistome genotypes such as mefA, msrD, mel, ant6, and tet40 increased in diversity and relative abundance following microcystin-LR exposure. Interestingly, the increased abundance of these genes was traced to resistance to common antibiotics such as tetracycline, macrolides, glycopeptide, and aminoglycosides, crucial for modern-day treatment of several diseases. Increased abundance of these genes was positively associated with increased expression of PD1, a T-cell homeostasis marker, and pleiotropic inflammatory cytokine IL-6 with a concomitant negative association with immunosurveillance markers IL-7 and TLR2. Microcystin-LR exposure also caused decreased TLR2, TLR4, and REG3G expressions, increased immunosenescence, and higher systemic levels of IL-6 in both wild-type and humanized mice. In conclusion, the results show a first-ever characterization of the host resistome following microcystin-LR exposure and its connection to host immune status and antimicrobial resistance that can be crucial to understand treatment options with antibiotics in microcystin-exposed subjects in clinical settings.

Intestinal microbiota profile in healthy Saudi children: The bacterial domain

Background

Knowledge of microbiota in health is essential for clinical research on the role of microbiota in disease. We aimed to characterize the intestinal microbiota in healthy Saudi children.

Methods

In this community-based study, stool samples were collected from a randomly selected sample of 20 healthy school children of Saudi origin. The samples were frozen at -80°C till analysis. Bacterial DNA was isolated and libraries were prepared using the Illumina Nextera XT library preparation kit. Unassembled sequencing reads were directly analyzed and quantified for each organism's relative abundance. The abundance for each organism was calculated and expressed as the average relative percentage from phyla to species.

Results

The median age was 11.3 (range 6.8-15.4) years, and 35% of them were males. The three most abundant phyla were Firmicutes, Bacteroidetes, and Actinobacteria accounting for 49%, 26%, and 24%, respectively. The most abundant genera included Bifidobacterium, Bacteroides, and Blautia accounting for 18.9%, 12.8%, and 8.2%, respectively. Finally, the most abundant species included 14 species belonging to the genus Bacteroides and nine species belonging to Bifidobacterium.

Conclusions

The abundance of intestinal microbiome in healthy Saudi children is different from that of other populations. Further studies are needed to understand the causes of variation between populations, which might lead to new preventive methods and treatment strategies of diseases caused by microbial dysbiosis.

Microbial Antagonism in Food-Enrichment Culture: Inhibition of Shiga Toxin-Producing Escherichia coli and Shigella Species

Bacterial pathogens, such as Shiga toxin-producing Escherichia coli (STEC) and Shigella spp., are important causes of foodborne illness internationally. Recovery of these organisms from foods is critical for food safety investigations to support attribution of illnesses to specific food commodities; however, isolation of bacterial cultures can be challenging. Methods for the isolation of STEC and Shigella spp. from foods typically require enrichment to amplify target organisms to detectable levels. Yet, during enrichment, target organisms can be outcompeted by other bacteria in food matrices due to faster growth rates, or through production of antimicrobial agents such as bacteriocins or bacteriophages. The purpose of this study was to evaluate the occurrence of Shigella and STEC inhibitors produced by food microbiota. The production of antimicrobial compounds in cell-free extracts from 200 bacterial strains and 332 food-enrichment broths was assessed. Cell-free extracts produced by 23 (11.5%) of the strains tested inhibited growth of at least one of the five Shigella and seven STEC indicator strains used in this study. Of the 332 enrichment broths tested, cell-free extracts from 25 (7.5%) samples inhibited growth of at least one of the indicator strains tested. Inhibition was most commonly associated with E. coli recovered from meat products. Most of the inhibiting compounds were determined to be proteinaceous (34 of the 48 positive samples, 71%; including 17 strains, 17 foods) based on inactivation by proteolytic enzymes, indicating presence of bacteriocins. The cell-free extracts from 13 samples (27%, eight strains, five foods) were determined to contain bacteriophages based on the observation of plaques in diluted extracts and/or resistance to proteolytic enzymes. These results indicate that the production of inhibitors by food microbiota may be an important challenge for the recovery of foodborne pathogens, particularly for Shigella sonnei. The performance of enrichment media for recovery of Shigella and STEC could be improved by mitigating the impact of inhibitors produced by food microbiota during the enrichment process.

Oral Microbiota Populations of Adult Dogs Consuming Wet or Dry Foods

Oral microbiota play a prominent role in canine periodontal disease and wet foods are often blamed for poor oral health, but canine oral microbial communities have been poorly studied. We aimed to determine differences in oral health measures, breath odor, and oral microbiota populations of dogs fed wet or dry food. Twelve adult dogs fed either a commercial dry (extruded) or commercial wet (canned) food for 6 wk were studied. Breath samples were measured for sulfur compounds, teeth were scored for plaque, calculus, and gingivitis by a blinded veterinary dentist, salivary pH was measured, and supragingival (SUP) and subgingival (SUB) plaque samples were collected for microbiota analysis. Plaque DNA was extracted and Illumina sequencing conducted. Phylogenetic data were analyzed using the CosmosID bioinformatics platform and SAS 9.4, with P<0.05 being significant and P<0.10 being trends. Plaque coverage tended to be higher (P<0.10) in dogs fed wet vs. dry food, but other oral health scores were not different. Dogs fed dry food had higher (P<0.05) salivary pH and lower (P<0.05) breath sulfur concentrations than those consuming wet food. Bacterial alpha diversity was higher in SUP than SUB samples, and a clear separation in beta diversity was observed between sample sites on principal coordinates analysis (PCoA) plots. In SUP samples, dogs fed wet food had a higher alpha diversity than dogs fed dry food, with PCoA plots showing a separation between wet and dry food. Relative abundances of Firmicutes, Synergistetes, and 10 bacterial genera were different (P<0.05) in SUB samples of dogs fed wet vs. dry food. Relative abundances of Fusobacteria and over 20 bacterial genera were different (P<0.05) in SUP samples of dogs fed wet vs. dry food. In general, oral health-associated bacterial taxa (Pasteurella, Capnocytophaga, Corynebacterium) were higher, while bacteria associated with poor oral health (Fretibacterium fastidiosum, Filifactor alocis, Treponema medium, Tannerella forsythia, Porphyromonas canoris, Porphyromonas gingivalis) were lower in dogs fed dry food. Such shifts in the oral microbiota may impact periodontal disease risk, but longer dietary intervention studies are required to confirm their role in the disease process. Our results suggest that dogs fed dry extruded foods have lower breath odor and tooth plaque buildup and an oral microbiota population more closely associated with oral health than dogs fed wet canned foods.

Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States

ABSTRACT

This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety.

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Next-generation sequencing: insights to advance clinical investigations of the microbiome

Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic sequencing, and RNA sequencing. The choice of which NGS methodology to pursue for a given purpose is often unclear for clinicians and researchers. In this Review, we describe the fundamentals of NGS, with a focus on 16S rRNA and shotgun metagenomic sequencing. We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disease pathophysiology across diverse clinical contexts, including the development of diagnostics and therapeutics. Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the coming years.

Analysis of the Ability of Capsaicin to Modulate the Human Gut Microbiota In Vitro

Previous studies on capsaicin, the bioactive compound in chili peppers, have shown that it may have a beneficial effect in vivo when part of a regular diet. These positive health benefits, including an anti-inflammatory potential and protective effects against obesity, are often attributed to the gut microbial community response to capsaicin. However, there is no consensus on the mechanism behind the protective effect of capsaicin. In this study, we used an in vitro model of the human gut microbiota to determine how regular consumption of capsaicin impacts the gut microbiota. Using a combination of NextGen sequencing and metabolomics, we found that regular capsaicin treatment changed the structure of the gut microbial community by increasing diversity and certain SCFA abundances, particularly butanoic acid. Through this study, we determined that the addition of capsaicin to the in vitro cultures of the human gut microbiome resulted in increased diversity of the microbial community and an increase in butanoic acid. These changes may be responsible for the health benefits associated with CAP consumption.

Metagenomics Approaches for Improving Food Safety: A Review

ABSTRACT

Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology.

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