What Differentiates Probiotic from Pathogenic Bacteria? The Genetic Mobility of Enterococcus faecium Offers New Molecular Insights

Genomic Characterization of Probiotic Purple Nonsulfur Bacteria Cereibacter sphaeroides Strains S3W10 and SS15: Implications for Enhanced Shrimp Aquaculture

Cereibacter sphaeroides strains S3W10 and SS15, isolated from shrimp ponds, exhibit potential probiotic benefits for aquaculture. In this study, the genomic features of S3W10 and SS15 were thoroughly characterized to evaluate their probiotic properties and safety for aquaculture use. The genomes of S3W10 and SS15 consist of 130 and 74 contigs, with sizes of 4.6 Mb and 4.4 Mb and GC contents of 69.2%. Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and phylogenomic analyses confirmed that these strains belong to C. sphaeroides. Genome annotation predicted 4260 coding sequences (CDS) in S3W10 and 4086 CDS in SS15, including genes associated with stress tolerance, nutrient absorption, and antioxidant activity. Notably, genes related to vitamin B12 synthesis, digestive enzyme production, and carotenoid biosynthesis, which support shrimp health, were identified in both genomes. CAZyme analysis identified 116 and 115 carbohydrate-active enzymes in S3W10 and SS15, respectively, supporting adaptation to gastrointestinal environments and the host immune response. Pan-genome analysis across C. sphaeroides strains revealed 7918 gene clusters, highlighting the open pan-genome structure of this species and its high genetic diversity. Further bioinformatic analyses assessing mobile genetic elements, antibiotic-resistance genes, and virulence factors demonstrated the safety of both strains for aquaculture, as no plasmids or virulence genes were identified. The genomic insights in this study provide a deeper understanding of the strains' adaptability and functional potential, aligning with previous in vitro and in vivo studies and highlighting their potential for use in shrimp cultivation.

Gene profile of virulence, antimicrobial resistance and action of enterocins in Campylobacter species isolated from broiler carcasses

Campylobacteriosis is among the most reported zoonoses in the world, caused by species of Campylobacter, this disease is characterized by gastroenteritis in humans. The main species involved is Campylobacter jejuni, followed by Campylobacter coli. Contaminated chicken meat is often identified as an important source of infection related to human cases and Brazil is the largest exporter of chicken meat in the world, which makes the characterization of brazilian isolates crucial for the establishment of control measures. The objective was to evaluate the contamination of chilled and frozen carcasses sold in the Northeast of Brazil, by Campylobacter species, identify virulence genes, evaluate bacterial resistance to antibiotics and verify the antimicrobial action of the Crude Extract Containing Enterocins (CECE) produced by a probiotic strain of Enterococcus faecium. In this study, 12 chilled carcasses and 12 frozen carcasses were collected, sold retail in supermarkets. The following regions of the carcass were sampled: breast skin, wing skin, belly skin, neck skin, gizzard and liver. Samples of chicken carcasses were analyzed following ISO 10272-2 guidelines for the isolation of Campylobacter spp. The isolates were tested by PCR to identify genus, species C. jejuni, C. coli and C. lari and genes cdtA, cdtB, cdtC, sodB, dnaJ, cmeA, cmeB, cmeC. The assessment of susceptibility to antibiotics was carried out using the standard disk diffusion method and the antimicrobial activity of CECE was determined using the Minimum Inhibitory Concentration (MIC), the methodologies followed the recommendations and cutoff points according to EUCAST and CLSI. A total of 376 isolates of Campylobacter spp. were obtained, among these, 26 (7.0%) were positive for C. jejuni and no isolates were detected for C. coli and C. lari. The highest frequency of C. jejuni was obtained in chilled carcasses with 23 isolates (88.5%, p < 0.0001), in frozen carcasses three isolates were obtained (11.5%). The most frequency site of C. jejuni was the chest skin (7/27.0%), followed by skin of the wing (6/23.0%), skin of the cloaca (5/19.0%), gizzard (4/15.0%), skin of the neck (2/8.0%) and liver (2/8.0%), no significant differences were found between the sites sampled. The gene frequency was determined in: cdtA (3/11.5%), cdtB (3/11.5%), cdtC (5/19.0%), sodB (9/34.5%), dnaJ (3/11.5%), cmeA (4/15.0%), cmeB (4/15.0%) and cmeC (4/15.0%). The three efflux pump genes were amplified in four isolates (15.3%) and all tested genes were amplified in three isolates (11.5%). All C. jejuni isolates (26/100.0%) were found to be multiresistant to three or more classes of antimicrobials. The index of multiple resistance to antimicrobial drugs (IRMA) ranged from 0.4 to 1.0 among isolates of C. jejuni. The antimicrobial activity of CECE was able to inhibit at least 98.5% of the growth of all C. jejuni isolates. Therefore, chilled chicken carcasses present a greater risk of contamination than frozen carcasses, for this reason it is necessary to adopt practices that avoid cross-contamination during the preparation of chicken meat, in order to prevent campylobacteriosis. Furthermore, the presence of multiresistant and potentially virulent isolates highlights the need for further investigations to better understand the use of enterocins as alternative methods in the control of Campylobacter.

Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product

The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.

Journey of the Probiotic Bacteria: Survival of the Fittest

This review aims to bring a more general view of the technological and biological challenges regarding production and use of probiotic bacteria in promoting human health. After a brief description of the current concepts, the challenges for the production at an industrial level are presented from the physiology of the central metabolism to the ability to face the main forms of stress in the industrial process. Once produced, these cells are processed to be commercialized in suspension or dried forms or added to food matrices. At this stage, the maintenance of cell viability and vitality is of paramount for the quality of the product. Powder products requires the development of strategies that ensure the integrity of components and cellular functions that allow complete recovery of cells at the time of consumption. Finally, once consumed, probiotic cells must face a very powerful set of physicochemical mechanisms within the body, which include enzymes, antibacterial molecules and sudden changes in pH. Understanding the action of these agents and the induction of cellular tolerance mechanisms is fundamental for the selection of increasingly efficient strains in order to survive from production to colonization of the intestinal tract and to promote the desired health benefits.

Pathogenic strains of Shewanella putrefaciens contain plasmids that are absent in the probiotic strain Pdp11

Shewanella putrefaciens Pdp11 is a strain described as a probiotic for use in aquaculture. However, S. putrefaciens includes strains reported to be pathogenic or saprophytic to fish. Although the probiotic trait has been related to the presence of a group of genes in its genome, the existence of plasmids that could determine the probiotic or pathogenic character of this bacterium is unknown. In the present work, we searched for plasmids in several strains of S. putrefaciens that differ in their pathogenic and probiotic character. Under the different conditions tested, plasmids were only found in two of the five pathogenic strains, but not in the probiotic strain nor in the two saprophytic strains tested. Using a workflow integrating Sanger and Illumina reads, the complete consensus sequences of the plasmids were obtained. Plasmids differed in one ORF and encoded a putative replication initiator protein of the repB family, as well as proteins related to plasmid stability and a toxin-antitoxin system. Phylogenetic analysis showed some similarity to functional repB proteins of other Shewanella species. The implication of these plasmids in the probiotic or pathogenic nature of S. putrefaciens is discussed.

Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers

Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18–30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.

Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2-6

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A cadmium resistant strain of Enterococcus faecium CX 2–6 is sequenced.

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Differential expression analysis found 47% of CX 2–6 genes are significantly affected by Cd treatment.

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Differentially expressed genes (DEGs) form physically linked gene clusters in the CX 2–6 genome.

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A prophage is unique to CX 2–6 and is strongly activated by high Cd concentration.

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A majority of DEGs responding to Cd treatment are present in the core genome.

Heavy metal pollutions in the soils are increasingly threatening the global crop and food production. Using plant associated bacteria to remediate heavy metal contamination is a promising approach. We have isolated a cadmium (Cd) resistant Enterococcus faecium strain CX 2–6 from a heavy metal contaminated farmland. We have shown that: (i) CX 2–6 can tolerate cadmium (Cd) with a slower growth rate; (ii) The CX 2–6 complete genome is fully assembled using PacBio long reads; (iii) Differential expression analysis found 47% of CX 2–6 genes are significantly affected by Cd treatment and form three gene groups with distinct expression profiles; (iv) Differentially expressed genes (DEGs) form physically linked gene clusters in the CX 2–6 genome, and one of the gene clusters corresponds to a prophage that is unique to CX 2–6 and is strongly activated when Cd concentration is higher; (v) A majority of DEGs responding to Cd treatment are present in the core genome; and (vi) 55 noncoding RNA genes are identified and 49 of them are DEGs responding to cadmium stress. Our pan-genome analysis and comparative RNA-seq data analysis has significantly improved our understanding of the metabolic reprogramming of E. faecium CX 2–6 under Cd stress.

Antarctic Strain of Rhodotorula mucilaginosa UFMGCB 18,377 Attenuates Mucositis Induced by 5-Fluorouracil in Mice

Mucositis is one of the most strenuous side effects caused by chemotherapy drugs, such as 5-fluorouracil (5-FU), during the treatment of several types of cancers. The disease is so prevalent and aggressive that many patients cannot resist such symptoms. However, despite its frequency and clinical significance, there is no effective treatment to prevent or treat mucositis. Thus, the use of probiotics as an adjuvant for the treatment has gained prominence. In the present study, we evaluated the effectiveness of oral administration of the Antarctic strain of Rhodotorula mucilaginosa UFMGCB 18,377 as an alternative to minimize side effects of 5-FU-induced mucositis in mice. Body weight, food consumption, stool consistency, and presence of blood in the feces were assessed daily in mice orally treated or not with the yeast and submitted or not to experimental mucositis. Blood, bones, and intestinal tissues and fluid were used to determine intestinal permeability and immunological, microbiological, and histopathological parameters. Treatment with R. mucilaginosa UFMGCB 18,377 was able to decrease clinical signs of the disease, such as reduction of food intake and body weight loss, and also decreased the number of intestinal enterobacteria and intestinal length shortening. Additionally, treatment was able to decrease the levels of MPO and EPO activities and inflammatory infiltrates, as well as the histopathological lesions characteristic of mucositis in the jejunum and ileum. Results of the present study showed that the oral administration of R. mucilaginosa UFMGCB 18,377 protected mice against mucositis induced by 5-FU.