Whole-genome sequencing and genomic-based acid tolerance mechanisms of Lactobacillus delbrueckii subsp. bulgaricus LJJ

Acid tolerance of Lactobacillus spp. on root carious lesions: A complex and multifaceted response

Lactobacillus spp. are acidogenic and aciduric bacteria and are among the main cariogenic microorganisms associated with the carious process.

OBJECTIVE

This study aimed to identify genes involved in the acid-tolerance of Lactobacillus spp. and potential functions attributed to these genes within the metatranscriptome of sound root surfaces and carious root surfaces.

DESIGN

Genomic libraries were built from mRNA isolated from the biofilm samples (10 from sound root and 9 from carious root using Illumina HiSeq 2500). Reads generated by RNA-seq were mapped against 162 oral microbial genomes and genes potentially related to acid tolerance were manually extracted from the Lactobacillus spp. genomes using L. paracasei ATCC 344 as reference genome. The R package DESeq2 was used to calculate the level of differential gene expression between those two clinical conditions.

RESULTS

Fifteen Lactobacillus spp. genomes were identified and a total of 653 acid tolerance genes were overexpressed in carious root surfaces. Multiple functions, as translation, ribosomal structure and biogenesis, transport of nucleotides and amino acids, are involved in Lactobacillus spp. acid tolerance. Species-specific functions also seem to be related to the fitness of Lactobacillus spp. in acidified environments such as that of the cariogenic biofilm associated with carious root lesions.

CONCLUSIONS

The response of Lactobacillus spp. to an acidic environment is complex and multifaceted. This finding suggests several possible avenues for further research into the adaptive mechanisms of these bacteria.

Comparative analysis of the transcriptional responses of Acetilactobacillus jinshanensis BJ01 to organic acids

As the important functional microorganism in the brewing process of Chinese Baijiu, lactic acid bacteria influences the microbial community and production of flavor substances in the Baijiu brewing process. In this study, we first isolated an Acetilactobacillus jinshanensis strain from baijiu fermented grains and named it A. jinshanensis BJ01. Its optimal growth conditions are 30 °C and pH 3.5. In particular, A. jinshanensis BJ01 cannot utilize inorganic acids and most organic acids, except for lactic acid (HL) and acetic acid (HAc). The observed phenotypes showed good growth with HL. When the mixed acid of HL-HAc (V:V = 1:1) was used, the growth rate of A. jinshanensis BJ01 greatly accelerated. Transcriptomic sequencing revealed the specific responses of the strain to the acidulants used. The number of upregulated genes in HL-HAc medium was more than that in single acid medium (HL or HAc). KEGG enrichment analyses indicated that the glycometabolism level of HAc regulation was relatively downregulated. The gene expression of quorum sensing and ABC transporter pathways were remarkably upregulated under HL-HAc regulation. Pyruvate metabolic pathway may be an important reason for the difference in A. jinshanensis BJ01 response to different organic acids. Our study reported a new organic acid-inducible growth type of bacteria mainly depending on the presence of HL and HAc, and was beneficial to the improvement of fermentation technology of Baijiu.

Insight into the acid tolerance mechanism of Acetilactobacillus jinshanensis subsp. aerogenes Z-1

Several lactic acid bacteria (LAB) are double-edged swords in the production of Sichuan bran vinegar; on the one hand, they are important for the flavour of the vinegar, but on the other hand, they result in vinegar deterioration because of their gas-producing features and their acid resistance. These characteristics intensify the difficulty in managing the safe production of vinegar using strains such as Acetilactobacillus jinshanensis subsp. aerogenes Z-1. Therefore, it is necessary to characterize the mechanisms underlying their acid tolerance. The results of this study showed a survival rate of 77.2% for Z-1 when exposed to pH 3.0 stress for 1 h. This strain could survive for approximately 15 days in a vinegar solution with 4% or 6% total acid content, and its growth was effectively enhanced by the addition of 10 mM of arginine (Arg). Under acidic stress, the relative content of the unsaturated fatty acid C18:1 (n-11) increased, and eight amino acids accumulated in the cells. Meanwhile, based on a transcriptome analysis, the genes glnA, carA/B, arcA, murE/F/G, fabD/H/G, DnaK, uvrA, opuA/C, fliy, ecfA2, dnaA and LuxS, mainly enriched in amino acid transport and metabolism, protein folding, DNA repair, and cell wall/membrane metabolism processes, were hypothesized to be acid resistance-related genes in Z-1. This work paves the way for further clarifying the acid tolerance mechanism of Z-1 and shares applicable perspectives for vinegar brewing.

Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People

The gut microbiome is one of the main factors affecting human health. It has been proven that probiotics can regulate the metabolism in the host body. A large number of people use probiotics not as medicines, but as a prophylactic supplement. The aim of our study was to evaluate the effect of lactic acid bacteria on the gut microbiome of healthy people using the V3 region of the 16S rRNA gene. Our study showed changes in the generic composition in the gut of healthy people when taking the supplement. There was an increase in the members responsible for the production of short-chain fatty acids in the gut of the host (Blautia, Fusicatenibacter, Eubacterium hallii group, Ruminococcus), as well as bacteria that improve intestinal homeostasis (Dorea and Barnesiella). There was also a decrease in the abundance of bacteria in the genera Catenibacterium, Hungatella, Escherichia-Shigella, and Pseudomonas, associated with an unhealthy profile of the human gut microbiome. An increase in members of the phylum Actinobacteriota was also observed, which has a positive effect on the host organism. Our results indicate that short-term prophylactic use of lactic acid bacteria-based supplements can be effective, as it contributes to a beneficial effect on the gut microbiome of healthy people.

Isolation and characterization of a gas-producing and acid-resistant bacterium from spoiled vinegar

To understand the deterioration of vinegar that has frequently occurred in China recently and to address such a concern, the physicochemical indicators and bacterial structure of the spoiled vinegar collected from Sichuan were preliminarily investigated. Results showed that Lactobacillaceae was most likely responsible for the decrease of vinegar total sugar and furfural, through which total acid and furfuryl alcohol were generated. Then, an unreported difficult-to-cultivate gas-producing bacterium named Z-1 was isolated using a modified MRS medium. Strain Z-1 was identified as Acetilactobacillus jinshanensis subsp. aerogenes on the basis of physiological, biochemical, molecular biological and whole genome analyses. According to the investigation, such species was present throughout the fermentation process and not limited in Sichuan. The analysis of genetic diversity indicated that all the obtained A. jinshanensis isolates displayed high sequence similarity and an absence of recombination. Although it demonstrated acid resistance, Z-1 could be completely deactivated through heating (60 °C). Based on the above results, suggestions for safe production are made for vinegar enterprises.

Comparative Genomics Analysis Provides New Insights into High Ethanol Tolerance of Lactiplantibacillus pentosus LTJ12, a Novel Strain Isolated from Chinese Baijiu

Lactic acid bacteria have received a significant amount of attention due to their probiotic characteristics. The species Lactiplantibacillus plantarum and Lactiplantibacillus pentosus are genotypically closely related, and their phenotypes are so similar that they are easily confused and mistaken. In the previous study, an ethanol-resistant strain, LTJ12, isolated from the fermented grains of soy sauce aroma type baijiu in North China, was originally identified as L. plantarum through a 16S rRNA sequence analysis. Here, the genome of strain LTJ12 was further sequenced using PacBio and Illumina sequencing technology to obtain a better understanding of the metabolic pathway underlying its resistance to ethanol stress. The results showed that the genome of strain LTJ12 was composed of one circular chromosome and three circular plasmids. The genome size is 3,512,307 bp with a GC content of 46.37%, and the number of predicted coding genes is 3248. Moreover, by comparing the coding genes with the GO (Gene Ontology), COG (Cluster of Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, the functional annotation of the genome and an assessment of the metabolic pathways were performed, with the results showing that strain LTJ12 has multiple genes that may be related to alcohol metabolism and probiotic-related genes. Antibiotic resistance gene analysis showed that there were few potential safety hazards. Further, after conducting the comparative genomics analysis, it was found that strain LTJ12 is L. pentosus but not L. plantarum, but it has more functional genes than other L. pentosus strains that are mainly related to carbohydrate transport and metabolism, transcription, replication, recombination and repair, signal transduction mechanisms, defense mechanisms and cell wall/membrane/envelope biogenesis. These unique functional genes, such as gene 2754 (encodes alcohol dehydrogenase), gene 3093 (encodes gamma-D-glutamyl-meso-diaminopimelate peptidase) and some others may enhance the ethanol tolerance and alcohol metabolism of the strain. Taken together, L. pentosus LTJ12 might be a potentially safe probiotic with a high ethanol tolerance and alcohol metabolism. The findings of this study will also shed light on the accurate identification and rational application of the Lactiplantibacillus species.

Genomic Characterization of Lactobacillus delbrueckii Strains with Probiotics Properties

Probiotics are health-beneficial microorganisms with mainly immunomodulatory and anti-inflammatory properties. Lactobacillus delbrueckii species is a common bacteria used in the dairy industry, and their benefits to hosting health have been reported. This study analyzed the core genome of nine strains of L. delbrueckii species with documented probiotic properties, focusing on genes related to their host health benefits. For this, a combined methodology including several software and databases (BPGA, SPAAN, BAGEL4, BioCyc, KEEG, and InterSPPI) was used to predict the most important characteristics related to L. delbrueckii strains probiose. Comparative genomics analyses revealed that L. delbrueckii probiotic strains shared essential genes related to acid and bile stress response and antimicrobial activity. Other standard features shared by these strains are surface layer proteins and extracellular proteins-encoding genes, with high adhesion profiles that interacted with human proteins of the inflammatory signaling pathways (TLR2/4-MAPK, TLR2/4-NF-κB, and NOD-like receptors). Among these, the PrtB serine protease appears to be a strong candidate responsible for the anti-inflammatory properties reported for these strains. Furthermore, genes with high proteolytic and metabolic activity able to produce beneficial metabolites, such as acetate, bioactive peptides, and B-complex vitamins were also identified. These findings suggest that these proteins can be essential in biological mechanisms related to probiotics’ beneficial effects of these strains in the host.

A review on the application of bioinformatics tools in food microbiome studies

There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.

In Vitro Probiotic Characteristics and Whole Genome Sequence Analysis of Lactobacillus Strains Isolated from Cattle-Yak Milk

Cattle-yak milk is an important raw material and an indispensable source of high-quality food for local farmers and herdsmen to produce ghee, milk residue, yogurt, and other dairy products. In this study, Lactobacillus strains were isolated from cattle-yak milk for potential probiotic candidates using a series of in vitro tests, including probiotic characterization and safety evaluation (antibiotic susceptibility and hemolytic ability). The results found that the Lactobacillus rhamnosus CY12 strain showed a high survival rate in bile salts, under acid conditions, and in the gastrointestinal juice environment, as well as showing high antimicrobial activity and adhesive potential. The safety evaluation showed that all strains were considered non-hemolytic. In addition, the whole-genome sequencing indicated that the strain CY12 spanned 2,506,167 bp, with an average length of 881 bp; the GC content in the gene region (%) was 47.35, contained 1347 protein-coding sequences, and accounted for 85.72% of the genome. The genome annotation showed that genes mainly focused on the immune system process, metabolic process, carbohydrate utilization, carbon metabolism, galactose metabolism, and biological adhesion, etc. This study revealed that the Lactobacillus rhamnosus CY12 strain might be an excellent potential probiotic in the development of feed additives for animals and has the ability to promote health.

Genome of Bifidobacterium longum NCIM 5672 provides insights into its acid-tolerance mechanism and probiotic properties

Bifidobacterium longum NCIM 5672 is a probiotic strain isolated from the Indian infant feces. The probiotic efficacy of Bifidobacteria is majorly affected by its acid tolerance. This study determined the probiotic properties and acid-tolerance mechanism of B. longum NCIM 5672 using whole-genome sequencing. The genome annotation is carried out using the RAST web server and NCBI PGAAP. The draft genome sequence of this strain, assembled in 63 contigs, consists of 22,46,978 base pairs, 1900 coding sequences and a GC content of 59.6%. The genome annotation revealed that seven candidate genes might be involved in regulating the acid tolerance of B. longum NCIM 5672. Furthermore, the presence of genes associated with immunomodulation and cell adhesion support the probiotic background of the strain. The analysis of candidate acid- tolerance-associated genes revealed three genes, argC, argH, and dapA, may play an essential role in high acid tolerance in B. longum NCIM 5672. The results of RT-qPCR supported this conclusion. Altogether, the results presented here supply an effective way to select acid-resistant strains for the food industry and provide new strategies to enhance this species' industrial applications and health-promoting properties.