Antimicrobial activity and safety features assessment of Weissella spp. from environmental sources

Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype

Antimicrobial resistance poses a serious threat to global public health. The COVID-19 pandemic underscored the need to monitor the dissemination of antimicrobial resistance genes and understand the mechanisms driving this process. In this study, we analyzed changes to the oropharyngeal and fecal resistomes of patients with COVID-19 undergoing therapy in a hospital setting. A targeted sequencing panel of 4,937 resistance genes was used to comprehensively characterize resistomes. Our results demonstrated that the oropharyngeal resistome is homogeneous, showing low variability over time. In contrast, fecal samples clustered into two distinct resistotypes that were only partially related to enterotypes. Approximately half of the patients changed their resistotype within a week of therapy, with the majority transitioning to a less diverse and ermB-dominated resistotype 2. Common macrolide resistance genes were identified in over 80% of both oropharyngeal and fecal samples, likely originating from streptococci. Our findings suggest that the fecal resistome is a dynamic system that can exist in certain "states" and is capable of transitioning from one state to another. To date, this is the first study to comprehensively describe the oropharyngeal resistome and its variability over time, and one of the first studies to demonstrate the temporal dynamics of the fecal resistotypes.

Gut microbiota in two chickens' breeds: Characteristics and dynamic changes

The gut microbiota has been demonstrated to play an important role in host immunity, metabolism, digestion, and growth. However, studies regarding the gut microbiota in Tibetan chickens remains scarce in comparison with other poultry breeds. Here, we investigated the gut microbial characteristics of Tibetan chickens and Arbor Acres broiler chickens (AA broiler chickens) and compare their gut microbial differences. For this purpose, we collected cecal samples from 10 Tibetan chickens and 10 AA broiler chickens for amplicon sequencing. Results indicated that Tibetan chickens exhibited higher gut microbial diversity and abundance compared with AA broiler chickens. Moreover, PCoA-based scatter plot analysis showed that the gut microbial structure of the both breeds was significantly different. Although the dominant bacterial phyla (Firmicutes, Firmicutes and Bacteroidota) of Tibetan chickens and AA broiler chickens were the same, the abundance of some bacterial phyla and genera changed significantly. Microbial taxonomic analysis indicated that the relative abundance of 876 genera of 20 phylum in Tibetan chickens increased significantly, while the relative abundance of 160 genera of 3 phyla decreased significantly compared with AA broiler chickens. In summary, these results indicated that there are significant differences in the gut microbiota between Tibetan chickens and AA broiler chickens. This is an important exploration of the gut microbial characteristics and distribution of Tibetan chickens. The findings may contribute to promoting the development of the Tibetan chicken's industry and reveal the adaptability of Tibetan chickens to the environment.

Evaluation of inhibitory, immunomodulatory, survival, and growth effects of host-derived Weissella confusa on Macrobrachium rosenbergii challenged with Vibrio parahaemolyticus

Macrobrachium rosenbergii is a highly valuable prawn species in aquaculture due to its current growing demand in the market. However, various bacterial diseases caused by Vibrio parahaemolyticus have been observed to induce mortality in larval, juvenile, and adult stages of M. rosenbergii. While antibiotics are commonly used to manage these diseases, they contribute to antimicrobial resistance, a global concern with serious environmental and health implications. Consequently, the scientific community is exploring host-derived beneficial microorganisms as functional feed additives, offering eco-friendly alternatives that boost shrimp and prawn immunity. The purpose of this study was to examine the effects of host-derived beneficial microorganisms from the gut of M. rosenbergii, on the inhibition, immunomodulation, survival, and growth of M. rosenbergii when exposed to V. parahaemolyticus. The result of this study showed that Weissella confusa C6, a lactic acid bacterium isolated from the gut of M. rosenbergii, significantly inhibits the growth of V. parahaemolyticus R1 as demonstrated in agar well diffusion assay and co-culture assay. Additionally, it showed immunomodulatory effects, indicated by elevated total hemocyte count (THC) and phenoloxidase (PO) activity during the bacterial challenge test. Furthermore, supplementing the diet with W. confusa led to significant improvements in M. rosenbergii, including increased survival rates, weight gain, specific growth rate, better feed conversion ratio, and reduced density of V. parahaemolyticus in the prawn's gut. Therefore, it can be considered a viable option for use as a feed supplement in prawn farming, enhancing M. rosenbergii's immune system, disease resistance, and overall health.

Evaluation of synbiotic combinations of commercial probiotic strains with different prebiotics in in vitro and ex vivo human gut microcosm model

Exploring probiotics for their crosstalk with the host microbiome through the fermentation of non-digestible dietary fibers (prebiotics) for their potential metabolic end-products, particularly short-chain fatty acids (SCFAs), is important for understanding the endogenous host-gut microbe interaction. This study was aimed at a systematic comparison of commercially available probiotics to understand their synergistic role with specific prebiotics in SCFAs production both in vitro and in the ex vivo gut microcosm model. Probiotic strains isolated from pharmacy products including Lactobacillus sporogenes (strain not labeled), Lactobacillus rhamnosus GG (ATCC53103), Streptococcus faecalis (T-110 JPC), Bacillus mesentericus (TO-AJPC), Bacillus clausii (SIN) and Saccharomyces boulardii (CNCM I-745) were assessed for their probiotic traits including survival, antibiotic susceptibility, and antibacterial activity against pathogenic strains. Our results showed that the microorganisms under study had strain-specific abilities to persist in human gastrointestinal conditions and varied anti-infective efficacy and antibiotic susceptibility. The probiotic strains displayed variation in the utilization of six different prebiotic substrates for their growth under aerobic and anaerobic conditions. Their prebiotic scores (PS) revealed which were the most suitable prebiotic carbohydrates for the growth of each strain and suggested xylooligosaccharide (XOS) was the poorest utilized among all. HPLC analysis revealed a versatile pattern of SCFAs produced as end-products of prebiotic fermentation by the strains which was influenced by growth conditions. Selected synbiotic (prebiotic and probiotic) combinations showing high PS and high total SCFAs production were tested in an ex vivo human gut microcosm model. Interestingly, significantly higher butyrate and propionate production was found only when synbiotics were applied as against when individual probiotic or prebiotics were applied alone. qRT-PCR analysis with specific primers showed that there was a significant increase in the abundance of lactobacilli and bifidobacteria with synbiotic blends compared to pre-, or probiotics alone. In conclusion, this work presents findings to suggest prebiotic combinations with different well-established probiotic strains that may be useful for developing effective synbiotic blends.

Characterization of Weissella Species during a 3-Year Observational Study - An Emerging Threat

Weissella species are mistaken for Lactobacillus or Leuconostoc because of their Gram-staining property and resistance to vancomycin. In this study, we aimed to evaluate the demographic pattern, presenting symptoms, risk factors, associated pathologies, and clinical outcomes in patients with Weissella infection. We also analyzed the antibiotic susceptibility pattern of the Weissella species isolated. This retrospective observational study was done from January 2021 to August 2023 in a tertiary care referral center in Uttar Pradesh. All Weissella species isolated from blood cultures or cerebrospinal fluid (CSF) samples during this period were included in the study. Twenty-four-hour growth from a positive blood culture or CSF sample was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Demographic and clinical details of the patients were extracted from the hospital information system. Kirby-Bauer disk diffusion was used for antibiotic susceptibility testing. During the 3-year study, 13 isolates of Weissella species were identified in our laboratory. Among the patients, male predominance was seen. The age range of the patients was 5-53 years. The samples were blood samples (n = 11) and CSF samples (n = 2). Of these isolates, 12 (92.3%) were identified as Weissella confusa and 1 (7.69%) was identified as Weissella viridescens. Common risk factors were anemia, prolonged hospital stay, indwelling catheter, chemotherapy, and chronic kidney disease. All the isolates in this study were sensitive to amikacin, daptomycin, amoxicillin-clavulanate, minocycline, and linezolid. Death was attributed to Weissella infection in three patients. Weissella species are opportunistic organisms that need to be identified quickly and precisely to guarantee the right course of treatment.

Detection of Vancomycin Resistant Genes in Intrinsically Antibiotic Resistant Bacteria from the Gut Microbiota of Indonesian Individuals

Background

Antibiotic resistance is a global public health concern that has been exacerbated by the overuse and misuse of antibiotics, leading to the emergence of resistant bacteria. The gut microbiota, often influenced by antibiotic usage, plays a crucial role in overall health. Therefore, this study aimed to investigate the prevalence of antibiotic resistant genes in the gut microbiota of Indonesian coastal and highland populations, as well as to identify vancomycin-resistant bacteria and their resistant genes.

Methods

Stool samples were collected from 22 individuals residing in Pacet, Mojokerto, and Kenjeran, Surabaya Indonesia in 2022. The read count of antibiotic resistant genes was analyzed in the collected samples, and the bacterium concentration was counted by plating on the antibiotic-containing agar plate. Vancomycin-resistant strains were further isolated, and the presence of vancomycin-resistant genes was detected using a multiplex polymerase chain reaction (PCR).

Results

The antibiotic resistant genes for tetracycline, aminoglycosides, macrolides, beta-lactams, and vancomycin were found in high frequency in all stool samples (100%) of the gut microbiota. Meanwhile, those meant for chloramphenicol and sulfonamides were found in 86% and 16% of the samples, respectively. Notably, vancomycin-resistant genes were found in 16 intrinsically resistant Gram-negative bacterial strains. Among the detected vancomycin-resistant genes, vanG was the most prevalent (27.3%), while vanA was the least prevalent (4.5%).

Conclusion

The presence of multiple vancomycin resistance genes in intrinsically resistant Gram-negative bacterial strains demonstrated the importance of the gut microbiota as a reservoir and hub for the horizontal transfer of antibiotic resistant genes.

Biotechnological Potential and Safety Evaluation of Dextran- and Riboflavin-Producing Weisella cibaria Strains for Gluten-Free Baking

Gluten consumption causes several immunological and non-immunological intolerances in susceptible individuals. In this study, the dextran-producing Weissella cibaria BAL3C-5 and its derivative, the riboflavin-overproducing strain BAL3C-5 C120T, together with a commercial bakery yeast, were used to ferment gluten-free (GF)-doughs obtained from corn and rice flours at two different concentrations and supplemented with either quinoa, buckwheat, or chickpea to obtain laboratory-scale GF bread. The levels of dextran, riboflavin, and total flavins were determined in the fermented and breads. Both strains grew in fermented doughs and contributed dextran, especially to those made with corn plus quinoa (~1 g/100 g). The highest riboflavin (350-150 µg/100 g) and total flavin (2.3-1.75 mg/100 g) levels were observed with BAL3C-5 C120T, though some differences were detected between the various doughs or breads, suggesting an impact of the type of flour used. The safety assessment confirmed the lack of pathogenic factors in the bacterial strains, such as hemolysin and gelatinase activity, as well as the genetic determinants for biogenic amine production. Some intrinsic resistance to antibiotics, including vancomycin and kanamycin, was found. These results indicated the microbiological safety of both W. cibaria strains and indicated their potential application in baking to produce GF bread.

Comparative genomics of 40 Weissella paramesenteroides strains

Weissella strains are often detected in spontaneously fermented foods. Because of their abilities to produce lactic acid and functional exopolysaccharides as well as their probiotic traits, Weissella spp. improve not only the sensorial properties but also nutritional values of the fermented food products. However, some Weissella species have been associated with human and animal diseases. In the era of vast genomic sequencing, new genomic/genome data are becoming available to the public on daily pace. Detailed genomic analyses are due to provide a full understanding of individual Weissella species. In this study, the genomes of six Weissella paramesenteroides strains were de novo sequenced. The genomes of 42 W. paramesenteroides strains were compared to discover their metabolic and functional potentials in food fermentation. Comparative genomics and metabolic pathway reconstructions revealed that W. paramesenteroides is a compact group of heterofermentative bacteria with good capacity of producing secondary metabolites and vitamin Bs. Since the strains rarely harbored plasmid DNA, they did not commonly possess the genes associated with bacteriocin production. All 42 strains were shown to bear vanT gene from the glycopeptide resistance gene cluster vanG. Yet none of the strains carried virulence genes.

Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species

Although numerous strains belonging to the Weissella genus have been described in the last decades for their probiotic and biotechnological potential, others are known to be opportunistic pathogens of humans and animals. Here, we investigated the probiotic potential of two Weissella and four Periweissella type strains belonging to the species Weissella diestrammenae, Weissella uvarum, Periweissella beninensis, Periweissella fabalis, Periweissella fabaria, and Periweissella ghanensis by genomic and phenotypic analyses, and performed a safety assessment of these strains. Based on the results of the survival to simulated gastrointestinal transit, autoaggregation and hydrophobicity characteristics, as well as adhesion to Caco-2 cells, we showed that the P. beninensis, P. fabalis, P. fabaria, P. ghanensis, and W. uvarum type strains exhibited a high probiotic potential. The safety assessment, based on the genomic analysis, performed by searching for virulence and antibiotic resistance genes, as well as on the phenotypic evaluation, by testing hemolytic activity and antibiotic susceptibility, allowed us to identify the P. beninensis type strain as a safe potential probiotic microorganism. IMPORTANCE A comprehensive analysis of safety and functional features of six Weissella and Periweissella type strains was performed. Our data demonstrated the probiotic potential of these species, indicating the P. beninensis type strain as the best candidate based on its potential probiotic features and the safety assessment. The presence of different antimicrobial resistance profiles in the analyzed strains highlighted the need to establish cutoff values to perform a standardized safety evaluation of these species, which, in our opinion, should be mandatory on a strain-specific basis.

Weissella and the two Janus faces of the genus

The genus Weissella belongs to the lactic acid bacteria group. It occurs naturally in foods and is a component of the human microbiome. A few Weissella species are candidate probiotics due to their potential for survival under the harsh conditions present in the gastrointestinal tract of humans and animals. Various species have also shown potential for treating and preventing periodontal disease, skin pathologies, and atopic dermatitis; some are used as starters for the fermentation of foods due to their production of exopolysaccharides; and others are used as protective cultures due to their production of weissellicin, a bacteriocin. However, a few Weissella species are opportunistic pathogens, such as W. ceti, which is the etiological agent of weissellosis, a disease in rainbow trout. Additionally, most Weissella species are intrinsically vancomycin-resistant. Thus, the Weissella genus is important from both medical and industrial points of view, and the Janus faces of this genus should be considered in any expected biotechnological applications. In this review, we present an overview of the probiotic potential and pathogenic cases of the Weissella genus reported in the literature.