Abundance Of Lactic Acid Bacteria Research Articles

Microbiological and Metagenomic Characterization of a Retail Delicatessen Galotyri-Like Fresh Acid-Curd Cheese Product

This study evaluated the microbial quality, safety, and ecology of a retail delicatessen Galotyri-like fresh acid-curd cheese traditionally produced by mixing fresh natural Greek yogurt with ‘Myzithrenio’, a naturally fermented and ripened whey cheese variety. Five retail cheese batches (mean pH 4.1) were analyzed for total and selective microbial counts, and 150 presumptive isolates of lactic acid bacteria (LAB) were characterized biochemically. Additionally, the most and the least diversified batches were subjected to a culture-independent 16S rRNA gene sequencing analysis. LAB prevailed in all cheeses followed by yeasts. Enterobacteria, pseudomonads, and staphylococci were present as <100 viable cells/g of cheese. The yogurt starters Streptococcus thermophilus and Lactobacillus delbrueckii were the most abundant LAB isolates, followed by nonstarter strains of Lactiplantibacillus, Lacticaseibacillus, Enterococcus faecium, E. faecalis, and Leuconostoc mesenteroides, whose isolation frequency was batch-dependent. Lactococcus lactis isolates were sporadic, except for one cheese batch. However, Lactococcus lactis, Enterobacteriaceae, Vibrionaceae, Salinivibrio, and Shewanellaceae were detected at fairly high relative abundances culture-independently, despite the fact that their viable counts in the cheeses were low or undetectable. Metagenomics confirmed the prevalence of S. thermophilus and Lb. delbrueckii. Overall, this delicatessen Galotyri-like cheese product was shown to be a rich pool of indigenous nonstarter LAB strains, which deserve further biotechnological investigation.

Exogenous enzymes and probiotics alter digestion kinetics, volatile fatty acid content and microbial interactions in the gut of Nile tilapia

Sustainable aquafeed production requires fishmeal replacement, leading to an increasing use of plant-derived ingredients. As a consequence, higher levels of antinutritional substances, such as non-starch polysaccharides and phytate, are present in aquafeeds, with negative effects on fish performance, nutrient digestibility and overall gut health. To alleviate these negative effects, providing exogenous digestive enzymes and/or probiotics can be an effective solution. In this study, we tested the effect of dietary supplementation of enzymes (phytase and xylanase) and probiotics (three strains of Bacillus amyloliquefaciens) on nutrient digestion kinetics and volatile fatty acid content along the gut, and the distal gut microbiome diversity in Nile tilapia. Chyme volatile fatty content was increased with probiotic supplementation in the proximal gut, while lactate content, measured for the first time in vivo in fish, decreased with enzymes along the gut. Enzyme supplementation enhanced crude protein, Ca and P digestibility in proximal and middle gut. Enzymes and probiotics supplementation enhanced microbial interactions as shown by network analysis, while increased the abundance of lactic acid bacteria and Bacillus species. Such results suggest that supplementation with exogenous enzymes and probiotics increases nutrient availability, while at the same time benefits gut health and contributes to a more stable microbiome environment.

Human Milk Microbiota in an Indigenous Population Is Associated with Maternal Factors, Stage of Lactation, and Breastfeeding Practices.

ABSTRACTBackgroundHuman milk contains a diverse community of bacteria that are modified by maternal factors, but whether these or other factors are similar in developing countries has not been explored. Our objective was to determine whether the milk microbiota was modified by maternal age, BMI, parity, lactation stage, subclinical mastitis (SCM), and breastfeeding practices in the first 6 mo of lactation in an indigenous population from Guatemala.MethodsFor this cross-sectional study, Mam-Mayan indigenous mothers nursing infants aged <6 mo were recruited. Unilateral human milk samples were collected (n = 86) and processed for 16S rRNA sequencing at the genus level. Microbial diversity and relative abundance were compared with maternal factors [age, BMI, parity, stage of lactation, SCM, and 3 breastfeeding practices (exclusive, predominant, mixed)] obtained through questionnaires.Results Streptococcus was the most abundant genus (33.8%), followed by Pseudomonas (18.7%) and Sphingobium (10.7%) but relative abundance was associated with maternal factors. First, Lactobacillus and Streptococcus were more abundant in early lactation whereas the common oral (Leptotrichia) and environmental (Comamonas) bacteria were more abundant in established lactation. Second, Streptococcus,Lactobacillus,Lactococcus,Leuconostoc, and Micrococcus had a higher abundance in multiparous mothers compared with primiparous mothers. Third, a more diverse microbiota characterized by a higher abundance of lactic acid bacteria (Lactobacillus,Leuconostoc, and Lactococcus), Leucobacter, and Micrococcus was found in mothers with a healthy BMI. Finally, distinct microbial communities differed by stage of lactation and by exclusive, predominant, or mixed breastfeeding practices.ConclusionMilk bacterial communities in an indigenous community were associated with maternal factors. Higher microbial diversity was supported by having a healthy BMI, the absence of SCM, and by breastfeeding. Interestingly, breastfeeding practices when assessed by lactation stage were associated with distinct microbiota profiles.

Bacterial Diversity in Pickled Cowpea (Vigna unguiculata [Linn.] Walp) as Determined by Illumina MiSeq Sequencing and Culture-Dependent Methods.

Pickled cowpea (Vigna unguiculata [Linn.] Walp) is a popular fermented vegetable in China that is made by spontaneous fermentation. Prior to this study, little was known about its microbial community. Eighteen pickled cowpea samples were collected in Enshi City, China, in 2018. The bacterial diversity within these samples was evaluated using a combination of high-throughput sequencing (Illumina MiSeq platform) targeting the V3-V4 region of the 16S rRNA gene sequence and culture-dependent methods. A total of 456,318 high-quality 16S rRNA gene sequence reads were obtained, and these reads were clustered into 19,712 OTUs with 97.0% similarity. The core bacterial phyla were Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes; the core bacterial genera were Levilactobacillus, Lactiplantibacillus, Companilactobacillus, Pediococcus, Lactobacillus, Weissella, and Pseudomonas. Using the spread-plating method, 39 lactic acid bacteria (LAB) strains were isolated and identified based on the nearly complete 16S rRNA gene sequence. Of these, 37 were identified as Lactiplantibacillus plantarum group, while the other two were classified as Limosilactobacillus fermentum and Lacticaseibacillus rhamnosus. These results indicate a high relative abundance of LAB in traditional pickled cowpea, especially Lactobacillaceae species, which likely contribute to fermentation. This study would provide information on the LAB population of Pickled cowpea and indicated that the Pickled cowpea could be a good source for isolation of lactic acid bacteria.

Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

The goal of the present study was to evaluate the effects of enzymes (cellulase combined with galactosidase) and their combination with Lactobacillus plantarum (LP) on bacterial diversity in alfalfa silages using high-throughput sequencing. Alfalfa forages were treated with or without cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), or ɑ-galactosidase + LP (GALP). After 56 days of ensiling, all treated silages exhibited improved fermentation quality, as reflected by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage (P < 0.05). Enzymatic treatment improved nutrient value by increasing crude protein levels and decreasing neutral detergent fibre (NDF) levels (P < 0.05). Silage treatment significantly altered the bacterial community, as determined by PCoA (P < 0.05). Lactic acid bacteria (LAB) dominated the bacterial community of the treated silage after ensiling. The dominant bacteria changed from Garciella, Enterococcus, Lactobacillus and Pediococcus in the control silage to Lactobacillus and Pediococcus in the CEGA silage and Lactobacillus in the CELP and GALP silages. Collectively, these results suggest that treatment with both enzymes alone and in combination with inoculants greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus observed in the silage treated with enzymes alone (CEGA) and Lactobacillus observed in the silage treated with a combination of enzymes and inoculants (CELP and GALP).

Characterizing microbial community and metabolites of Cantonese soy sauce

The present researches aimed to investigate the difference of metabolites and the microbial community diversity among batches of Cantonese soy sauce. These results indicated that a higher abundance of lactic acid bacteria, such as Weissella, Lactobacillus originated from koji, in the initial moromi inhibited functional microbes' propagating and metabolizing, wild fungi became dominant. Therefore, the contents of dominant metabolites, including non-volatiles and volatiles as well as their species identified were significantly different. The content of dominant volatiles (Odor Activity Value, OAV >1) were 47.81%, 58.36% and 58.13%, respectively in batch 1, batch 2 and batch 3. This volatiles included ethanol, 3-methyl-1-butanol, 1-octen-3-ol, phenethyl alcohol, acetic acid, 4-ethyl guaiacol. Compared with batch 1, the contents of acetic acid and Ala increased, while that of Glu and esters decreased significantly in the samples of the other two batches. Their flavor characteristics were different from the commercial samples’ based on the Orthogonal Partial Least Squares Discrimination Analysis (OPLS-DA) and Principal Component Analysis (PCA) results due to higher content of acetic acid. Meanwhile, the strength of enzymes expression related with dominant compounds was differentiated. These results were conducive to regulating the process so that improving the quality of soy sauce.

Microbiome of industrialized Minas Frescal Cheese reveals high prevalence of putative bacteria: A concern in the One Health context

The knowledge about microbiota from cheeses plays a key role in safety improvement and quality enhancement of the final product. We used a high throughput sequencing methodology to provide insights into the microbial composition of Minas Frescal Cheese (MFC). The results obtained from the analysis of 28 cheese samples showed that cheeses were brand-clustered, exhibiting unique bacterial profiles which varied in diversity and abundance of taxa. Proteobacteria dominated in all samples, corresponding to a mean of 88.7% from all sequences. Groups associated with contamination, as Pseudomonas, Acinetobacter and Vibrio were highly frequent in most of brands. Low abundance of lactic acid bacteria was also observed. The core microbiome shared by 100% of the samples indicated predominance of Enterobacteriaceae family. Our data point to a concern regarding the occurrence of potential spoilage microbiota and opportunistic pathogens in cheeses. This metataxonomic study suggests correlations between putative bacteria and antimicrobial resistance phenomenon in foodstuff, as already reported for MFC. Together these data highlight that productive chain of MFC might be related to spread of medically important bacteria, which are underestimated for their possible impact on human health. The observations may also reinforce the importance of food safety regulations facing the One Health point of view.

Dietary Lipid:Protein Ratio and n-3 Long-Chain Polyunsaturated Fatty Acids Alters the Gut Microbiome of Atlantic Salmon Under Hypoxic and Normoxic Conditions.

Researchers have adjusted dietary lipid:protein ratios and n-3 long-chain polyunsaturated fatty acids (LC-PUFA) to optimize the growth performance of Atlantic salmon. However, dietary impacts on the gut microbiome are lacking, especially under varying environmental conditions. To examine this response, post-smolt salmon (184 ± 5 g) were fed diets with lipid:protein ratios considered low (180, 570 g/kg) and high (230, 460 g/kg) along with low and high levels of n-3 LC-PUFA (7 or 14 g/kg) while fish were reared under low and high levels of dissolved oxygen (6.7 or 8.0 mg/L). At day 0, 35 and 116, digesta in the distal intestine were collected and analyzed for viable counts and 16S ribosomal RNA (rRNA) genes (V4 region) using Illumina MiSeq. The reduction in oxygen had negligible effects, except on viable plate counts of total bacteria and an initial effect on beta-diversity. In contrast, the high lipid (HL) diets had an increased alpha-diversity (e.g., Shannon and Chao-1) at day 0 and day 35 whereas high n-3 diets suppressed these indices at day 116. Generally, a reduction in alpha-diversity was observed over time and an interaction between lipid:protein ratio x n-3 was found. Between diets, beta-diversity and phyla abundance were similar as both Proteobacteria (44%) and Firmicutes (21%) dominated. However, at the genus level Aliivibrio, Streptococcus, Weissella, and Lactobacillus, were associated with low lipid (LL) diets while the high lipid diets were associated with less abundant bacteria, e.g., Chromohalobacter. At day 116, the relative abundance of the Tenericutes phylum increased 10-fold (36%). Fish fed the high lipid diet with high n-3 had reduced alpha-diversity, lowest abundance of lactic acid bacteria, and highest abundance of Mycoplasma, which may indicate a less healthy gut microbiome. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed that saturated and unsaturated fatty acid biosynthesis pathways were several folds higher in fish fed the high lipid diet, possibly to compensate for the lack of dietary n-3. In summary, our results show that the viable plate counts, alpha-diversity, beta-diversity, and predictive function of gut bacteria in Atlantic salmon post-smolts are influenced by dietary lipid:protein ratio and n-3 LC-PUFA over several time points with little effect by dissolved oxygen.

Effect of static magnetic field on microbial community during anaerobic digestion

Dairy wastewater is characterized by high concentration of organic compounds and is commonly used for energy production. Methods for enhancement of biogas production include application of magnetizers on the digester to induce static magnetic field (SMF). The study aimed at investigation of Bacteria and Archaea communities during anaerobic digestion of model dairy wastewater exposed to SMF. Magnetic field caused a significant increase in methane production to 373.2 mL/g VS compared to 200.2 mL/g VS in a control reactor and methane content to 56.8% compared to 49.1% in a control reactor. In both reactors, the biomass was dominated by Trichococcus sp. The relative abundance of lactic acid bacteria was of about 10% higher in the reactor exposed to SMF. This higher number of Lactobacillales resulted from a higher acetate production, which additionally caused enhanced growth of Methanosarcinacaea in the reactor exposed to SMF. SMF also stimulated the growth of hydrogenotrophic methanogens.

Relationships between the bacterial diversity and metabolites of a Chinese fermented pork product, sour meat

SummaryThe present study evaluated the relationship between the bacterial diversity and metabolites of various sour meats, a traditional fermented meat product. The results showed that sour meats had a low pH (average of 4.34), low water activity (aw, an average of 0.917), and high lactic acid (~19 177.48 mg kg−1) and free amino acid (FAA) (~4047.65 mg kg−1) concentrations. The lactic acid bacteria (LAB), especiallyLactobacillusandWeissella, were predominated in the samples. The alcohols, aldehydes and esters accounted for the major components of volatile organic compounds (VOCs). Of which, (E)‐2‐octenal, nerol, cis‐4‐decenal, tetradecanal, linalyl acetate, linalool, 1‐octen‐3‐ol, hexanal, 1‐heptanol, benzaldehyde and (E)‐2‐decenal were considered as the key VOCs of sour meats. The redundancy analysis (RDA) and Pearson’s correlation analysis revealed that LAB (LactobacillusandWeissella) and salt were positively correlated with most FAAs and VOCs. Overall, higher salinity, lowerawand abundant LAB might be the indicators of good sour meat quality.

Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata).

BackgroundIn the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6).MethodsA 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ± 0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt.Results and ConclusionsThe feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were associated with the 60% CO diet. However, lower abundance of lactic acid bacteria, specifically Lactobacillus, in the gut of fish fed the 60% CO diet may indicate a potential negative effect on gut microbiota. PICRUSt analysis revealed similar predictive functions of bacteria in the faeces and mucosa, although a higher abundance of Corynebacterium in the mucosa of fish fed 60% CO diet increased the KEGG pathway of fatty acid synthesis and may act to compensate for the lack of fatty acids in the diet. In summary, this study demonstrated that up to 40% of FO can be replaced with CO without negative effects on growth performance, fillet composition and gut microbiota of gilthead sea bream.

Changes in the Gut Microbiome after Galacto-Oligosaccharide Administration in Loperamide-Induced Constipation.

Unbalanced dietary habits and the consumption of high protein and instant foods cause an increase in constipation. Here, we evaluated the effects of galacto-oligosaccharide (GOS) on a rat model of loperamide-induced constipation by measuring various biological markers and cecal microbiota. The fecal water content and intestinal transit ratio significantly increased in the GOS-administered (GL and GH) groups than in the control group (p < 0.05, p < 0.01, and p < 0.001, respectively). The length of intestinal mucosa (p < 0.05 and p < 0.01, respectively) and area of crypt cells were (p < 0.01, both) significantly increased in the GOS-administered groups compared to the control group. The distribution of interstitial cells of Cajal, which is related to the intestinal movement, showed a significant increase in GOS-administered groups than in the control group (p < 0.01, both). The relative abundance of lactic acid bacteria (LAB), especially Lactobacillus and Lactococcus, significantly increased in the GL group than in the control group. Furthermore, there was a positive correlation between short chain fatty acids (SCFAs) and the gut microbiota in the GL groups. These results demonstrated that GOS administration effectively alleviates constipation by increasing LAB proliferation in the intestinal microbiota and SCFA production.

The Use of Less Conventional Meats or Meat with High pH Can Lead to the Growth of Undesirable Microorganisms during Natural Meat Fermentation.

The bacterial communities that are established during natural meat fermentation depend on the processing conditions and the type of meat substrate used. Six pork samples of variable quality (reflected in pH values) and six less conventional meats (beef, horse, hare, wild deer, wild duck, and wild boar) were naturally fermented under controlled conditions in model systems. The development of lactic acid bacteria (LAB), coagulase-negative staphylococci (CNS), and enterobacteria was followed using culture-dependent techniques and (GTG)5-PCR fingerprinting of genomic DNA from the isolates obtained. Taken together, Latilactobacillus sakei was the most abundant LAB species, although Latilactobacillus curvatus was more manifest in high-pH pork. Within staphylococci, common species were encountered (i.e., Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus), although some atypical ones (i.e., Staphylococcus succinus) were also recovered. Within enterobacteria, Serratia spp. prevailed in more acidic pork batches and in beef, whereas Hafnia spp. prevailed in game meat fermentations. Enterobacterial counts were particularly high in fermentations with low acidity, namely for some pork batches, hare, wild duck, and wild boar. These findings should be considered when naturally fermented meat products are manufactured, as the use of game meat or meat with high pH can give rise to safety concerns.

Postbiotic and Anti-aflatoxigenic Capabilities of Lactobacillus kunkeei as the Potential Probiotic LAB Isolated from the Natural Honey

The use of probiotic, postbiotic, and anti-aflatoxigenic capabilities of the lactic acid bacteria (LAB) isolated from stressful niches is a major strategy to prepare functional cultures and bio-preservatives for food industries. In the present study, abundant LAB strains isolated from natural honey were screened based on their tolerance to continuous pH and bile salt treatments. Then, the pro-functional properties of the selected LAB were investigated. In accordance with the screening data, a bacilli isolate was selected for further characterization. Sequencing results led to the identification of Lactobacillus kunkeei as the selected LAB isolate. In vitro antibacterial and antifungal activities of the LAB and in situ antifungal activity of the isolate cell-free supernatant (CFS) were verified against food-borne indicators. Accordingly, in vitro antibacterial and antifungal effects of Lact. kunkeei ENH01 on respective Escherichia coli and Aspergillus niger were significantly (P < 0.05) higher than the other indicators. Furthermore, in situ inhibitory effect of Lact. kunkeei CFS on Candida albicans (as the highest in situ effect) was equal to 76.36%. The presence of three antibacterial peptides was also verified in the Lact. kunkeei CFS according to the results of liquid chromatography mass spectrometry (LC/MS) assay. Antibiotic susceptibility profile and auto-aggregation ability of the isolate were noticeable. Anti-mycotoxigenic capabilities of Lact. kunkeei ENH01 as viable and heat-killed cells were also revealed against total aflatoxins according to the HPLC-based analysis. In vivo safety of the isolate was also attested through the evaluation of blood biochemistry and hematological parameters in the Lact. kunkeei ENH01 fed-mice compared with the control. Based on the findings, probiotic properties of Lact. kunkeei ENH01 and postbiotic capabilities of the isolate CFS and its heat-killed cells were approved.

Silage Fermentation: A Potential Biological Approach for the Long-Term Preservation and Recycling of Polyphenols and Terpenes in Globe Artichoke (Cynara scolymus L.) By-Products.

An economic and effective method for storage is necessary to make full use of the nature of active components in artichoke by-products and ease environmental pressure. In this paper, the potential of silage fermentation for the preservation and recycling of polyphenols and terpenes in artichoke by-products is evaluated. The silage of artichoke by-products is characterized by lactic acid bacteria fermentation. Silage distinctly increases the abundance of lactic acid bacteria in artichoke by-products, such as Lactobacillus, Lactococcus, Serratia, and Weissella, and greatly increases the abundance of Firmicutes. The improvement of the microorgan structure and composition is of great significance for the quality of artichoke by-products. Polyphenols in the stems and leaves of artichokes are preserved well in silage. Among the 18 polyphenol compounds detected by high performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (HPLC-QqQ-MS/MS), the contents of 11 phenolic acids and four flavonoids increased significantly. For terpenes detected by gas chromatography-mass spectrometry (GC-MS), the contents of four pentacyclic triterpenoids increased significantly, while two sterols were kept stable in the silage process. Silage is a potential biotechnology for the long-term preservation of bioactive components, such as polyphenols and terpenes in artichoke by-products, and the results provide a scientific basis for the efficient utilization of by-products.

Diversity of lactic acid bacteria in Moutai-flavor liquor fermentation process

ABSTRACT Maotai-flavor liquor, derived from a multi-stage solid fermentation process, is one of the most popular liquors in China. Its quality and flavor are closely related to diverse lactic acid bacteria (LAB). It is therefore significant to characterize LAB for the manufacturing of Maotai-flavor liquor. In this study, LAB in solid state fermentation stages were analyzed through high-throughput sequencing and cultivation-dependent methods during the fermentation process. In total, 65 LAB species were identified in the fermented matrix, showing a much higher LAB diversity than other types of Chinese liquor. In addition, discrepancies were found to exist in the dominant LAB community structures during different fermentation stages, and strains of the Lactobacillus genus were found to be the most dominant LAB. Furthermore, 33 LAB species were identified from the fermentation matrix through the cultivation and 16 S rRNA analysis of single isolates, thus representing 50.8% coverage of the detected LAB species. The relative abundance of isolated LAB in the total abundance of LAB was 95.9% during the fermentation process. In doing so, Lac2 and Lac13, two potentially new LAB species, were isolated. To the best of our knowledge, this study represents the identification of the highest number of LAB species by cultivation-dependent methods from fermented grains of Chinese liquor. In summary, this study monitored the LAB species composition of solid fermented matrix during the fermentation of Maotai-flavor liquor and has highlighted the potential importance of the higher abundance of LAB and the effect it has on the unique flavor of Maotai liquor.

In silico mapping of microbial communities and stress responses in a porcine slaughterhouse and pork products through its production chain, and the efficacy of HLE disinfectant

The use of shotgun metagenomic sequencing to understand ecological-level spread of microbes and their genes has provided new insights for the prevention, surveillance and control of microbial contaminants in the slaughterhouse environment. Here, microbial samples were collected from products and surrounding areas though a porcine slaughter process; shotgun metagenomic DNA-sequencing of these samples revealed a high community diversity within the porcine slaughterhouse and pork products, in zones originating from animal arrival through to the sale zones. Bacteria were more prevalent in the first zones, such as arrival- and anesthesia-zones, and DNA viruses were prevalent in the scorching-and-whip zone, animal products and sale zone. Data revealed the dominance of Firmicutes and Proteobacteria phyla followed by Actinobacteria, with a clear shift in the relative abundance of lactic acid bacteria (mainly Lactobacillus sp.) from early slaughtering steps to Proteobacteria and then to viruses suggesting site-specific community compositions occur in the slaughterhouse. Porcine-type-C oncovirus was the main virus found in slaughterhouse, which causes malignant diseases in animals and humans. As such, to guarantee food safety in a slaughterhouse, a better decipher of ecology and adaptation strategies of microbes becomes crucial. Analysis of functional genes further revealed high abundance of diverse genes associated with stress, especially in early zones (animal and environmental surfaces of arrival zone with 57,710 and 40,806 genes, respectively); SOS responsive genes represented the most prevalent, possibly associated with genomic changes responsible of biofilm formation, stringent response, heat shock, antimicrobial production and antibiotic response. The presence of several antibiotic resistance genes suggests horizontal gene transfer, thus increasing the likelihood for resistance selection in human pathogens. These findings are of great concern, with the suggestion to focus control measures and establish good disinfection strategies to avoid gene spread and microbial contaminants (bacteria and viruses) from the animal surface into the food chain and environment, which was achieved by applying HLE disinfectant after washing with detergent.

Salinity and fish age affect the gut microbiota of farmed Chinook salmon (Oncorhynchus tshawytscha)

Detailed classification and characterisation of the gut microbial community and understanding of factors affecting the microbiota are essential to understand the relationship between Chinook salmon (Oncorhynchus tshawytscha) gut microbiota and fish health. Here we evaluated the multiple effects of biotic and abiotic factors on the gut microbial community composition of farmed Chinook salmon, based on high-throughput sequencing of 16S rRNA gene V1-V3 amplicons. Gastrointestinal microbial community composition was highly dynamic between freshwater and saltwater conditions but similar among individual fish. A high abundance of Proteobacteria and a relatively low abundance of lactic acid bacteria (LAB) were detected in farmed Chinook salmon regardless of salinity. Species richness and diversity were significantly higher in freshwater farmed salmon than in those farmed in the marine environment. Water temperature and farming location displayed relatively minor effects on gut microbiota, while fish age had significant effects on the beta diversity of gut microbiota in both freshwater and saltwater habitats. Our study provided a detailed description of the gut microbial community of farmed Chinook salmon during grow out and contributed to a greater understanding of the effects of fish age and water salinity on the gut microbiota modulation.

High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens.

Microbial contamination of dairy products with a high fat content (e.g., butter) has been studied insufficiently. No studies using modern molecular methods to investigate microbial communities in butter have been conducted so far. In this work, we used high-throughput sequencing and Sanger sequencing of individual bacterial colonies to analyze microbial content of commercially available butter brands. A total of 21 samples of commercially available butter brands were analyzed. We identified a total of 94 amplicon sequence variants corresponding to different microbial taxa. The most abundant lactic acid bacteria in butter were Lactobacillus kefiri, Lactobacillus parakefiri, Lactococcus taiwanensis and Lactococcus raffinolactis. A large amount of Streptococcus spp. bacteria (87.9% of all identified bacteria) was found in one of the butter samples. Opportunistic pathogens such as Bacillus cereus group, Pseudomonas aeruginosa, Cronobacter spp., Escherichia coli, Listeria innocua, Citrobacter spp., Enterococcus spp., Klebsiella pneumonia were detected. The analyzed butter samples were most strongly contaminated with bacteria from the Bacillus cereus group, and to a lesser extent - with Cronobacter spp. and Enterococcus spp. The plating and Sanger sequencing of individual colonies revealed the presence of Enterobacter cloacae and Staphylococcus epidermidis. The Sanger sequencing also showed the presence of Cronobacter sakazakii in butter which can be dangerous for children under the age of 1 year. We demonstrated that butter is a good growth medium for opportunistic pathogenic bacteria. Our data indicate that despite the fact that butter is a dairy product with a long shelf life, it should be subjected to quality control for the presence of opportunistic bacteria.

Green Tea and Pomegranate Extract Administered During Critical Moments of the Production Cycle Improves Blood Antiradical Activity and Alters Cecal Microbial Ecology of Broiler Chickens.

Phytobiotics are usually tested in feed and throughout the production cycle. However, it could be beneficial to evaluate their effects when administered only during critical moments, such as changes in feeding phases. The aim of the trial was to investigate the effect of a commercial plant extract (PE; IQV-10-P01, InQpharm Animal Health, Kuala Lumpur, Malaysia) on growth performance, blood antiradical activity and cecal microbiome when administered in drinking water to broiler chickens during the post-hatching phase and at each change of diet. In the experiment, 480 1-day-old male broiler chicks were assigned to two groups in a 50-day trial. Broilers received drinking water (C) or drinking water plus PE (T) at a rate of 2 mL/L on days 0 to 4, 10-11 and 20-21. PE did not affect performance and water intake, while total antiradical activity was improved (p < 0.05). A greater abundance of lactic acid bacteria (false discovery rate (FDR) < 0.05) was found in the T group and the result was confirmed at a lower taxonomic level with higher Lactobacillaceae abundance (FDR < 0.05). Our findings suggest that PE administration during critical moments of the production cycle of broiler chickens may exert beneficial effects at a systemic level and on gut microbial ecology.