Safety assessment of Gram-negative bacteria associated with traditional French cheeses

Gut symbiotic bacteria are involved in nitrogen recycling in the tephritid fruit fly Bactrocera dorsalis

Background

Nitrogen is considered the most limiting nutrient element for herbivorous insects. To alleviate nitrogen limitation, insects have evolved various symbiotically mediated strategies that enable them to colonize nitrogen-poor habitats or exploit nitrogen-poor diets. In frugivorous tephritid larvae developing in fruit pulp under nitrogen stress, it remains largely unknown how nitrogen is obtained and larval development is completed.

Results

In this study, we used metagenomics and metatranscriptomics sequencing technologies as well as in vitro verification tests to uncover the mechanism underlying the nitrogen exploitation in the larvae of Bactrocera dorsalis. Our results showed that nitrogenous waste recycling (NWR) could be successfully driven by symbiotic bacteria, including Enterobacterales, Lactobacillales, Orbales, Pseudomonadales, Flavobacteriales, and Bacteroidales. In this process, urea hydrolysis in the larval gut was mainly mediated by Morganella morganii and Klebsiella oxytoca. In addition, core bacteria mediated essential amino acid (arginine excluded) biosynthesis by ammonium assimilation and transamination.

Conclusions

Symbiotic bacteria contribute to nitrogen transformation in the larvae of B. dorsalis in fruit pulp. Our findings suggest that the pattern of NWR is more likely to be applied by B. dorsalis, and M. morganii, K. oxytoca, and other urease-positive strains play vital roles in hydrolysing nitrogenous waste and providing metabolizable nitrogen for B. dorsalis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01399-9.

Evaluation of the Potential Probiotic Yeast Characteristics with Anti-MRSA Abilities

Methicillin-resistant Staphylococcus aureus (MRSA) is a disreputable pathogenic bacterium that has been proven to colonize the intestinal tract. The goal of this study is to find anti-MRSA probiotic yeast from food and evaluate its probiotic characteristics and safety. Finally, 15 strains were isolated from fruit peel with anti-MRSA ability. Using DNA sequence analysis, they were identified as the genus Hanseniaspora (7 strains) and Starmerella (8 strains). Starmerella bacillaris CC-PT4 (CGMCC No. 23573) that was isolated from the grape peel has good auto-aggregation ability and hydrophobicity, and can tolerate 0.3% bile, pH 2, simulated gastric fluid (SGF), and simulated intestinal fluid (SIF). Strikingly, Starmerella bacillaris CC-PT4, like commercial probiotic Saccharomyces boulardii CNCM I-745 (Florastor ^®), can adapt to the temperature of the human body (37 ℃). After safety assessment, this strain is sensitive to amphotericin B and cannot produced β-hemolytic activities. Overall, this study provides a new candidate for probiotic yeast with anti-MRSA ability.

Providencia heimbachae Associated with Post-weaning Diarrhea in Piglets: Identification, Phenotype, and Pathogenesis

Despites Providencia heimbachae has been isolated from human, penguin, and bovine fetus, relatively little information is available regarding the pathogenicity and biologic characteristics of P. heimbachae. Here, we report that investigation of post-weaning diarrhea yielded bacterial isolates identified as P. heimbachae based on the biochemical tests and 16S ribosomal DNA sequence analysis. The two isolates were positive for utilization of Malonate, no gas production from glucose, and non-fermentation of D-mannitol, D-Galactose, and L-Rhamnose that were different from those of the type strain, and both of them have the ability of adhesion and invasion to IPEC-J2 cells, and were resistant to 21 out of the 41 antibiotics tested. In addition, the isolate 99101 was highly pathogenic to mice and piglets. Histopathology studies on nerve tissue of piglets that developed hindlimb paralysis showed microglia cell infiltration and neuron damage in the spinal cord. Notably, the strains could grow under low temperature (4 °C), which raise attention of a new risk factor for food safety. To the best of our knowledge, this is the first report of P. heimbachae strain caused post-weaning diarrhea in piglets in both natural and experimental conditions. These findings extended the knowledge of P. heimbachae as an important zoonotic agent, which should be given more attention during surveillance and diagnostics.

Microbiology of Hafnia alvei

Hafnia alvei is a Gram-negative facultatively anaerobic bacillus that constitutes part of the human gut flora. Until recently, H. alvei strains could be mistakenly identified by conventional methods, miniaturisation or automatic systems as members of the Serratia, Escherichia, Citrobacter, Yokenella, Obesumbacterium or Salmonella genera. Consequently, molecular techniques were required for their definitive identification in the clinical laboratory. In addition, a new Hafnia species, H. paralvei, has recently appeared, which undoubtedly includes many of the strains reported in the literature as H. alvei. Alrhough H. alvei isolation from human clinical specimens remains uncommon, the development of drug resistance due to this species is emerging and it is likely that this organism will gain increasing importance in the future. Moreover, although H. alvei shares some virulence mechanisms with other Gram-negative enteropathogens, little is known about the factors that contribute to its pathogenesis in humans. The present article reviews the current identification methods, antimicrobial resistance and virulence factors of this bacterium.

Temporal differences in microbial composition of Époisses cheese rinds during ripening and storage

Époisses is a protected designation of origin smear-ripened cheese from the Burgundy region in France. It has an orange color and a strong flavor, both of which are generated by surface microorganisms. The objective of the present study was to investigate the microbial dynamics at the surface of Époisses cheese during ripening and postmanufacturing storage at low temperatures. Rind samples were analyzed by enumeration on agar plates and by 16S rRNA gene and internal transcribed spacer amplicon sequencing. During most of the ripening process, the counts of yeasts, which corresponded to the species Debaryomyces hansenii and Geotrichum candidum, were higher than those of the aerobic acid-sensitive bacteria. Debaryomyces hansenii reached a level of about 3 × 10⁸ cfu/cm², and its viability strongly decreased in the late stage of ripening and during storage at 4°C. Two of the inoculated bacterial species, Brevibacterium aurantiacum and Staphylococcus xylosus, did not establish themselves at the cheese surface. At the end of ripening, among the 18 most abundant bacterial species detected by amplicon sequencing, 14 were gram-negative, mainly from genera Psychrobacter, Vibrio, Halomonas, and Mesonia. It was hypothesized that the high moisture level of the Époisses rinds, due the humid atmosphere of the ripening rooms and to the frequent washings of the curds, favored growth of these gram-negative species. These species may be of interest for the development of efficient ripening cultures. In addition, because the orange color of Époisses cheeses could not be attributed to the growth of Brevibacterium, it would be interesting to investigate the type and origin of the pigments that confer color to this cheese.

Metaproteomics insights into traditional fermented foods and beverages

Traditional fermented foods and beverages (TFFB) are important dietary components. Multi-omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi-omics technology requires further integration to reveal the molecular nature of TFFB fermentation.

Comparison of bacterial communities in gliadin-degraded sourdough (Khamir) sample and non-degraded sample

The study was undertaken to investigate the comparison lying between bacterial communities in autochthonous gliadin-degraded sourdough sample (D13) and non-degraded sample (D50). Degree of gliadin degradation in various samples was determined by Fourier transform infrared spectroscopy and represented samples were selected for 16 S rDNA sequence analysis by Illumina Miseq platform. It was observed, that Proteobacteria (50.65%) and Actinobacteria (6.70%) phyla were more abundant as compared with Firmicutes (42.53%) in D13, however, Firmicutes (83.44) were more abundant, comparatively, in D50 than Proteobacteria (14.97%). Lower taxonomic levels surfaced its more prominent effects. It had been also observed that Lactobacillus genera was the core genera (50.37%) followed by Weissella (27.15%) and Psychrobacter (21.53%) in D50 and D13, respectively. Shannon and Simpson indices indicated that degraded sample had more bacterial diversity and richness compared with non-degraded sample.

[The greater wax moth, Galleria mellonella to study host-pathogen interactions]

The massive use of antibiotics in health and agriculture has led to the emergence of pathogenic microorganisms resistant to frequently used treatments. In 2017, the World Health Organization (WHO) published its first ever list of antibiotic-resistant "priority pathogens", a catalogue of twelve families of bacteria that pose the greatest threat to human health. In this context, a new model for the study of host-pathogen interactions is becoming increasingly popular : the greater wax moth, Galleria mellonella. This butterfly larvae, sometimes considered as a new "laboratory rat", has many practical advantages and is an important host in the study of some steps in the pathogenicity of infectious agents and the identification of new treatments. This review presents this alternative model and describes its possible applications.