Academic literature on the topic 'Lactobacillales – Biodiversité'

This study shows the potential of probiotic dairy product to modulate the gut microbiota. The effect of the product on the intestinal microflora was determined by examining the fecal microflora of rats before and after 4 weeks of adding a fermented milk probiotic product to the diet. Structural changes in the faecal microflora were studied on the basis of sequencing V1-V3 hypervariable target region 16S rRNA gene. Sequencing results showed a decrease in microbiota biodiversity after taking a probiotic product. Nevertheless, enrichment of the microflora with butyrate-producing microorganisms Lachnospiraceae, Ruminococcaceae, Lactobacillales and depletion of Porphyromonadaceae, Eggerthella, Romboutsia, Fusicatenibacter and Bacillus, which are not belong to the order Lactobacillales.

Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals.

The gut microbiota and its development for the health of pets are currently being actively developed. The composition of the gut microbiome is found in the reduction of food intake, the state of the immune system of animals, productivity and growth in livestock content. Also found in the colon are unusual pathogen phyla that can serve as markers of fecal contamination in the environment. We conducted a study of the intestinal microbiome of 12 animals divided into two groups - calves and adult cows. Bacteria of taxa of taxa Actinobacteriota, Bacteroidota, Campilobacterota, Chloroflexi, Cyanobacteria, Desulfobacterota, Fibrobacterota, Firmicutes, Fusobacterota, Halobacterota, Elusimicrobiota, Euryarchaeota, Proteobacteria, Patescibacteria, Spirochaetota, Thermoplasmatota, Verrucomicrobia and a large number of unclassified bacteria were identified.It has been shown that the intestinal microbiome of calves differs from that of adult cows, and diarrhea affects the composition of the intestines of young animals, reducing the biodiversity of the inhabitants. In calves, the Shannon index ranged from 3.18 to 4.3, in adult animals from 4.41 to 5.24. Comparison of the gut microbiomes of healthy calves and calves with diarrhea was carried out using the Hutcheson t-test, the difference was significant (P<<<0.0001). > The main phyla of calf intestinal bacteria are Bacteroidota and Firmicutes, moreover, the diversity and number of microbial lines of Bacteroidota increases with age. Firmicutes of the families Lactobacillae and Lactobacillales_fa, as well as the family Selenomonadaceae, are markers of the juvenile age of animals. Calf-specific Bacteroidota are representatives of Tannerellaceae and Marinifilaceae. The microbiome of adult animals at the phylum level is distinguished by the presence of bacteria Verrucomicrobiota, Desulfobacterota, archaea Methanobacteria and Methanomicrobia. At the level of families and genera, the formed microbiome of cows has unique representatives of Bacteroidota and Firmicutes.Thus, we have presented data on the main representatives of healthy intestinal bacteria of cows and calves, which can later be used to diagnose the physiological state of animals, as well as in environmental studies to detect fecal environmental pollution.

Abstract. Manguntungi B, Saputri DS, Mustopa AZ, Ekawati N, Afgani CA, Sari AP, Triratna L, Sukmarini L, Fatimah, Kusmiran A, Yanti S, Irawan S, Prasetyo MD, Fidien KA. 2020. Metagenomic analysis and biodiversity of Lactic Acid Bacteria (LAB) on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia. Biodiversitas 21: 3287-3293. Masin is a spontaneously fermented sauce from Sumbawa, West Nusa Tenggara Indonesia that is made of shrimp paste, chili, turmeric flower, and herbs mixed with some spices. This study aims to isolate Lactic Acid Bacteria (LAB) and analyze the metagenomic and biodiversity of its bacteria. Genome isolation for metagenomic analysis was using ZymoBIOMICSTM DNA Miniprep Kit. Sequencing analysis to identify LAB strain form masin was using 16S rRNA universal primer. Metagenomic analysis showed that relative abundance bacteria in masin for order taxon was Lactobacillales, the family taxon was Enteroccocaceae, and the genus was Tetragenoccocus. Six different groups were obtained from the phylogenetic tree analysis of 40 isolates found in masin. The representatives of each group taken were isolates number 2, 17, 11, 34, 28, and 5. Based on the results of sequencing analysis, the 6 isolates found in masin are Staphylococcus piscifermentans strain CIP103958 (Isolate Code 2), S. piscifermentans strain BULST54 (Isolate Code 17), S. piscifermentans strain SK03 (Isolate Code 11), S. piscifermentans strain ATCC 51136 (Isolate Code 34), S. piscifermentans strain PCM 2409 (Isolate Code 28) and S. piscifermentans strain PU-87 (Isolate Code 5). Through this research, it has been described a whole diversity of bacteria contained in masin, one of them is Lactic acid bacteria. The six LAB isolates that have been identified can be developed as starter candidates for masin production.

AbstractThe increasing amount of weeds surviving herbicide represents a very serious problem for crop management. The interaction between microbial community of soil and herbicide resistance, along with the potential evolutive consequences, are still poorly known and need to be investigated to better understand the impact on agricultural management. In our study, we analyzed the microbial composition of soils in 32 farms, located in the Northern Italy rice-growing area (Lombardy) with the aim to evaluate the relationship between the microbial composition and the incidence of resistance to acetolactate synthase (ALS) and acetyl-CoA carboxylase (ACCase) inhibiting herbicides in Echinochloa species. We observed that the coverage of weeds survived herbicide treatment was higher than 60% in paddy fields with a low microbial biodiversity and less than 5% in those with a high microbial biodiversity. Fungal communities showed a greater reduction in richness than Bacteria. In soils with a reduced microbial diversity, a significant increase of some bacterial and fungal orders (i.e. Lactobacillales, Malasseziales and Diaporthales) was observed. Interestingly, we identified two different microbial profiles linked to the two conditions: high incidence of herbicide resistance (H-HeR) and low incidence of herbicide resistance (L-HeR). Overall, the results we obtained allow us to make hypotheses on the greater or lesser probability of herbicide resistance occurrence based on the composition of the soil microbiome and especially on the degree of biodiversity of the microbial communities.

The vaginal microbiota plays a key role in animals’ health. Understanding its diversity and composition and associated changes occurring through the reproductive cycle represents valuable knowledge to disclose the mechanisms leading to dysbiosis and eventually to infection. Even if the human vaginal microbiota has been thoroughly studied, scarce research has been conducted on the vaginal microbiota of livestock. In this study, 16S rRNA gene-based sequencing was performed on vaginal samples of ten nulliparous ewes at three different sampling points: before the estrus synchronization protocol (T0), at the time of estrus before mating (Testrus), and the day of the pregnancy diagnosis (Tpreg). Preputial samples from the three males collected pre and post-mating were also analyzed. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the most abundant phyla in vaginal samples. The most abundant genera were Porphyromonas, Anaerococcus, and Peptinophilius. Vaginal microbiota biodiversity decreased during pregnancy. Tenericutes (Ureaplasma spp.) increased significantly at Tpreg in both pregnant and non-pregnant ewes. Differences were observed between pregnant and non-pregnant ewes at Tpreg where pregnant ewes had a significantly higher abundance of Actinobacillus spp. and Ureaplasma spp. Ewes that were diagnosed with pregnancy at Tpreg showed a decreased abundance of gram-negative bacteria such as Bacteroidales, Campylobacterales, and Enterobacteriales. In addition, a significant decrease in the relative abundances of genera within Firmicutes, such as Alloicoccus (Lactobacillales), Atopostipes (Lactobacillales), and an uncultured bacteria W5053 from Family XI (Firmicutes, Clostridiales) was observed in non-pregnant ewes at Tpreg. The four most abundant phyla in the rams’ prepuce were the same as in the ewes’ vagina. The most abundant genus was Corynebacterium. No major differences were observed in the ram’s preputial microbiota between pre and post-mating samples. Nevertheless, the differences in the taxonomic composition of ewes’ vaginal microbiota between Testrus and Tpreg could be explained by the exposure to the preputial microbiota. This study offers new insights into the effects of several key steps of the ewe’s reproductive cycle such as estrus-synchronization protocol, mating, and pregnancy on ovine vaginal microbiota. The knowledge of the microbiota dynamics during the reproductive cycle can help improve the reproductive outcomes of dams by identifying biomarkers and putative probiotics.

Oenococcus oeni est une espèce de bactéries lactiques (BL) adaptée aux conditions difficiles du vin. Sa spécialisation lui permet de survivre et proliférer dans des environnements caractérisés par un pH acide et des teneurs en éthanol élevéesl, où la plupart des autres bactéries ne peuvent pas se développer. O. oeni joue un rôle crucial dans la production de vin en réalisant la fermentation malolactique (FML) qui suit la fermentation alcoolique (FA). Durant la MLF, l'acide malique est converti en acide lactique, ce qui adoucis le goût du vin. Le génome d'O. oeni mute plus rapidement que celui d'autres espèces de BL, en raison de l’absence de gènes de réparation de l’ADN mutS/L. Cette hyper-mutabilité pourrait avoir favorisé son adaptation au vin. Les centaines de souches séquencées à ce jour forment 4 lignées génétiques adaptées à différents produits : vin (lignée A), moût et cidre (lignées B et C), et kombucha (lignée D).Les vins de distillation de Cognac représentent une niche écologique spécifique pour O. oeni, en raison de leur pH bas, de la non-utilisation de sulfites, et de la période de stockage prolongée suivant la FA jusqu'à la distillation. Cette thèse visait à explorer la biodiversité d'O. oeni et des autres BL durant leur production. Le génotypage d'isolats d'O. oeni, le séquençage de génomes et la qPCR des vins nous ont permis d'identifier une nouvelle sous-lignée génétique, nommée AC, qui est prédominante durant la FML (Chapitre 1).Les analyses phénotypiques ont révélé que les souches AC ont une meilleure croissance en milieu acide (pH 3.0) que des souches commerciales de la lignée A. De plus, pendant la FML, les souches AC influencent différemment le métabolome des vins, produisant moins de lactate d'éthyle et consommant moins de sucres résiduels que les souches A. La génomique comparative a montré que les souches AC partagent certains gènes uniques qui suggèrent notamment un métabolisme spécifique du sucre. De plus, l'analyse de la distribution des gènes d'exopolysaccharides a mis en évidence une structure génétique spécifique des souches AC par rapport aux autres souches A (Chapitre 2).La dynamique des populations d'O. oeni et des BL a été étudiée durant le stockage du vin de la MLF à la distillation, par métabarcoding, phylogénomique et qPCR. La persistance des souches d'O. oeni dans les caves a également été suivie sur quatre millésimes. Les résultats ont montré qu'O. oeni restait l'espèce dominante au sein de la communauté bactérienne pendant la conservation des vins. Les souches AC étaient généralement les souches prédominantes tout au long de la conservation. Les souches AC étaient également les bactéries les plus persistantes dans les caves durant plusieurs millésimes (Chapitre 3).Dans la mesure où les vins de distillation sont produits sans sulfites ajoutés, ils sont sujets aux altérations bactériennes pendant leur conservation. La diversité des bactéries dans les vins de Cognac altérés par l’acroléine a été étudiée par identification des espèces (MALDI-TOF MS, metabarcoding), et des souches (MLVA et RAPD), révélant la présence d'espèces telles que Lactobacillus paracasei, L. hilgardii et O. oeni à différents niveaux de population. Un opéron pdu a été identifié pour la première fois chez une souche d'O. oeni. Cet opéron permet la conversion du glycérol en acroléine, qui confère un goût amer aux eaux-de-vie après distillation des vins. Un test de qPCR a été développé pour détecter les bactéries qui portent cet opéron dans les vins (Chapitre 4).Cette étude enrichit notre compréhension de la biodiversité des BL dans les vins de distillation de Cognac, en particulier la biodiversité de l'espèce O. oeni et sa dynamique de population, ouvrant la voie à de futures stratégies visant à améliorer l'impact bénéfique d'O. oeni durant la MLF dans ces vins, et à prédire et prévenir leur altération, améliorant ainsi la qualité du cognac
Oenococcus oeni is a lactic acid bacteria (LAB) species adapted to the challenging conditions of wine. Its specialization enables survival and proliferation in environments characterized by low pH and high ethanol levels, where most other bacteria cannot thrive. O. oeni plays a critical role in wine production by executing the malolactic fermentation (MLF) which follows the alcoholic fermentation (AF). During MLF, malic acid is converted into lactic acid, thereby softening the taste of wine. The genome of O. oeni mutates faster than that of other LAB species, primarily due to the absence of DNA mismatch repair genes. This high mutation rate is thought to have favored its adaptation to wine. The hundreds of strains sequenced to date form 4 genetic lineages adapted to different products: wine (lineage A), must and cider (lineages B and C), and kombucha (lineage D).Distillation wines from Cognac represent a specific ecological niche for O. oeni, due to their low pH, the non-utilization of sulfites, and the extended storage period following AF until distillation. This thesis aimed to explore the biodiversity of O. oeni and other LAB during their production. Genotyping of thousands of O. oeni isolates, genome sequencing of about 50 strains and qPCR analyses of the wines allowed us to identify a new genetic sub-lineage, named AC, which is predominant during MLF (Chapter 1).Phenotypic analyses revealed that AC strains exhibit superior growth in acidic conditions (pH 3.0) in Ugni blanc must, compared to commercial strains from lineage A. Furthermore, during MLF, AC strains influence the metabolic profile of wines differently, producing less ethyl lactate and consuming fewer residual sugars than A strains. Comparative genomics of the AC strains showed that they share some unique genes, such as α/β-fold hydrolase enzymes, biotin synthesis proteins, an arabinose-proton symporter and a D-xylose transporter, suggesting a specific sugar metabolism. Analyzing the distribution of exopolysaccharides genes further highlighted a specific genetic structure of AC strains compared to other A strains (Chapter 2).The population dynamics of O. oeni and LAB was monitored during wine storage from MLF to distillation by metabarcoding, phylogenomics, and qPCR. The persistence of O. oeni strains in cellars was also monitored over four consecutive vintages. Results showed that O. oeni remained the dominant species within the bacterial community during the conservation of Cognac wines. AC strains were usually the predominant strains throughout the storage period. AC strains were also the most persistent bacteria in cellars during several vintages (Chapter 3).Incidents of contaminations with Lactobacillus hilgardii, suggesting potential spoilage post-MLF, were observed in two wine samples. Given that distillation wines are produced without added sulfites, they are subject to bacterial spoilage during the long storage period that precedes distillation. The diversity of bacteria in spoiled Cognac wines was investigated by identification of species (MALDI-TOF MS, metabarcoding), and strain genotyping (MLVA, RAPD), revealing the presence of LAB species such as Lactobacillus paracasei, L. hilgardii, and O. oeni at different population levels. A pdu operon was identified for the first time in one of the sequenced O. oeni strains. This operon encodes genes for the conversion of glycerol into acrolein, which confers bitterness to the wine. A qPCR assay was developed for the early detection of bacteria in wine that carry this operon (Chapter 4).This study enriches our understanding of LAB biodiversity in Cognac distillation wines, particularly the biodiversity of the species O. oeni and its population dynamics, paving the way for future strategies aimed at improving the beneficial impact of O. oeni during MLF in these wines, and predicting and preventing their spoilage, thereby enhancing the quality of cognac