Comparative genomic analysis of Lactobacillus mucosae LM1 identifies potential niche-specific genes and pathways for gastrointestinal adaptation

A metagenomic approach to unveil the association between fecal gut microbiota and short-chain fatty acids in diarrhea caused by diarrheagenic Escherichia coli in children

Diarrheagenic Escherichia coli (DEC) is the main cause of diarrhea in children under five years old. The virulence of DEC is tightly regulated by environmental signals influenced by the gut microbiota and its metabolites. Short-chain fatty acids (SCFAs) are the main metabolic product of anaerobic fermentation in the gut, but their role in DEC diarrhea has not yet been established. In this study, we determine the levels of acetate, propionate, and butyrate in stool samples from children with diarrhea caused by DEC, and we identify bacteria from the fecal gut microbiota associated with the production of SCFAs. The microbiota and SCFAs levels in stool samples obtained from 40 children with diarrhea and 43 healthy children were determined by 16S rRNA gene sequencing and HPLC, respectively. Additionally, shotgun metagenomics was used to identify metagenome-assembled genomes (MAGs) in a subgroup of samples. The results showed significantly higher levels of all SCFAs tested in diarrheal samples than in healthy controls. The abundance of Streptococcus sp., Limosilactobacillus, Blautia, Escherichia, Bacteroides, Megamonas, and Roseburia was higher in the DEC group than in healthy individuals. Functional analysis of bacteria and their main metabolic pathways made it possible to identify species MAGs that could be responsible for the detected SCFAs levels in DEC-positive diarrhea. In conclusion, based on our results and published data, we suggest that SCFAs may be important in the crosstalk between the microbiota and DEC pathogens in the gut.

Alterations of fecal microbiome and metabolome in pemphigus patients

The role of gut microbiome and metabolic substances in the development of autoimmune diseases has gradually been revealed. However, the relevant gut features in pemphigus have not been well clarified. We collected stool samples from pemphigus patients and healthy controls (HCs). Metagenomic sequencing and liquid chromatography-mass spectrometry (LC/MS) metabolome sequencing were performed to analyze the compositional and metabolic alternations of the gut microbiome in pemphigus patients and HCs. We observed the reduced richness and diversity and greater heterogeneity in pemphigus patients, which was characterized by a significant decrease in Firmicutes and an increase in Proteobacteria. At the species level, Intestinal pathogenic bacteria such as Escherichia coli and Bacteroides fragilis were significantly enriched, while anti-inflammatory bacteria and butyric acid-producing bacteria were significantly reduced, which were related to clinical indicators (Dsg1/3 and PDAI). 4 species were selected by the machine learning algorithm to better distinguish pemphigus patients from healthy people. Metabolomic analysis showed that the composition of pemphigus patients was different from that of HCs. PE (18:3 (6Z,9Z, 12Z)/14:1 (9Z)) was the main metabolic substance in pemphigus and involved in a variety of metabolic pathways. While Retinol, flavonoid compounds and various amino acids decreased significantly compared with HCs. Furthermore, we found that differences in the levels of these metabolites correlated with changes in the abundance of specific species. Our study provides a comprehensive picture of gut microbiota and metabolites in pemphigus patients and suggests a potential mechanism of the aberrant gut microbiota and metabolites in the pathogenesis of pemphigus.

Synthesis of the Hexasaccharide Related to the Exopolysaccharide from Lactobacillus mucosae VG1 through Regioselective Glycosylation

Chemical synthesis of the hexasaccharide repeating unit associated with the exopolysaccharide of Lactobacillus mucosae VG1 is reported. The total synthesis is accomplished through a convergent [2 + 2 + 2] strategy using rationally protected monosaccharide derivatives. Chemoselective activation of the glycosyl donors and regioselective nucleophilicity of the acceptors were successfully employed throughout the chemical synthesis.

Isolation and Characterization of Lactic Acid Bacteria With Probiotic Attributes From Different Parts of the Gastrointestinal Tract of Free-living Wild Boars in Hungary

Lactic acid bacteria (LAB) in the microbiota play an important role in human and animal health and, when used as probiotics, can contribute to an increased growth performance in livestock management. Animals living in their native habitat can serve as natural sources of microorganisms, so isolation of LAB strains from wild boars could provide the opportunity to develop effective probiotics to improve production in swine industry. In this study, the probiotic potential of 56 LAB isolates, originated from the ileum, colon, caecum and faeces of 5 wild boars, were assessed in vitro in details. Their taxonomic identity at species level and their antibacterial activity against four representative strains of potentially pathogenic bacteria were determined. The ability to tolerate low pH and bile salt, antibiotic susceptibility, bile salt hydrolase activity and lack of hemolysis were tested. Draft genome sequences of ten Limosilactobacillus mucosae and three Leuconostoc suionicum strains were determined. Bioinformatic analysis excluded the presence of any known acquired antibiotic resistance genes. Three genes, encoding mesentericin B105 and two different bacteriocin-IIc class proteins, as well as two genes with possible involvement in mesentericin secretion (mesE) and transport (mesD) were identified in two L. suionicum strains. Lam29 protein, a component of an ABC transporter with proved function as mucin- and epithelial cell-adhesion factor, and a bile salt hydrolase gene were found in all ten L. mucosae genomes. Comprehensive reconsideration of all data helps to select candidate strains to assess their probiotic potential further in animal experiments.

Arsenic-Containing Medicine Treatment Disturbed the Human Intestinal Microbial Flora

Human intestinal microbiome plays vital role in maintaining intestinal homeostasis and interacting with xenobiotics. Few investigations have been conducted to understand the effect of arsenic-containing medicine exposure on gut microbiome. Most animal experiments are onerous in terms of time and resources and not in line with the international effort to reduce animal experiments. We explored the overall microbial flora by 16S rRNA genes analysis in fecal samples from acute promyelocytic leukemia (APL) patients treated with arsenic trioxide (ATO) plus all-trans retinoic acid (ATRA). Gut microbiomes were found to be overwhelmingly dominated by Firmicutes and Bacteroidetes after taking medicines containing arsenic in APL patients. The fecal microbiota composition of APL patients after treatment showed lower diversity and uniformity shown by the alpha diversity indices of Chao, Shannon, and Simpson. Gut microbiome operational taxonomic unit (OTU) numbers were associated with arsenic in the feces. We evaluated Bifidobacterium adolescentis and Lactobacillus mucosae to be a keystone in APL patients after treatment. Bacteroides at phylum or genus taxonomic levels were consistently affected after treatment. In the most common gut bacteria Bacteroides fragilis, arsenic resistance genes were significantly induced by arsenic exposure in anaerobic pure culture experiments. Without an animal model, without taking arsenicals passively, the results evidence that arsenic exposure by drug treatment is not only associated with alterations in intestinal microbiome development at the abundance and diversity level, but also induced arsenic biotransformation genes (ABGs) at the function levels which may even extend to arsenic-related health outcomes in APL.

Bioinformatics and its role in the study of the evolution and probiotic potential of lactic acid bacteria

Due to their numerous well-established applications in the food industry, there have been many studies regarding the adaptation and evolution of lactic acid bacteria (LAB) in a wide variety of hosts and environments. Progress in sequencing technology and continual decreases in its costs have led to the availability of LAB genome sequence data. Bioinformatics has been central to the extraction of valuable information from these raw genome sequence data. This paper presents the roles of bioinformatics tools and databases in understanding the adaptation and evolution of LAB, as well as the bioinformatics methods used in the initial screening of LAB for probiotic potential. Moreover, the advantages, challenges, and limitations of employing bioinformatics for these purposes are discussed.

Maturation of the gut metabolome during the first year of life in humans

The gut microbiota is involved in the production of numerous metabolites that maintain host wellbeing. The assembly of the gut microbiome is highly dynamic, and influenced by many postnatal factors, moreover, little is known about the development of the gut metabolome. We showed that geography has an important influence on the microbiome dynamics in the first year of life based on two independent cohorts from China and Sweden. Major compositional differences since birth were the high relative abundance of Bacteroides in the Swedish cohort and Streptococcus in the Chinese cohort. We analyzed the development of the fecal metabolome in the first year of life in the Chinese cohort. Lipid metabolism, especially acylcarnitines and bile acids, was the most abundant metabolic pathway in the newborn gut. Delivery mode and feeding induced particular differences in the gut metabolome since birth. In contrast to C-section newborns, medium- and long-chain acylcarnitines were abundant at newborn age only in vaginally delivered infants, associated by the presence of bacteria such as Bacteroides vulgatus and Parabacteroides merdae. Our data provide a basis for understanding the maturation of the fecal metabolome and the metabolic role of gut microbiota in infancy.

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.

Systematic evaluation of genome-wide metabolic landscapes in lactic acid bacteria reveals diet- and strain-specific probiotic idiosyncrasies

Lactic acid bacteria (LAB) are well known to elicit health benefits in humans, but their functional metabolic landscapes remain unexplored. Here, we analyze differences in growth, intestinal persistence, and postbiotic biosynthesis of six representative LAB and their interactions with 15 gut bacteria under 11 dietary regimes by combining multi-omics and in silico modeling. We confirmed predictions on short-term persistence of LAB and their interactions with commensals using cecal microbiome abundance and spent-medium experiments. Our analyses indicate that probiotic attributes are both diet and species specific and cannot be solely explained using genomics. For example, although both Lacticaseibacillus casei and Lactiplantibacillus plantarum encode similarly sized genomes with diverse capabilities, L. casei exhibits a more desirable phenotype. In addition, "high-fat/low-carb" diets more likely lead to detrimental outcomes for most LAB. Collectively, our results highlight that probiotics are not "one size fits all" health supplements and lay the foundation for personalized probiotic design.

Phenotype-genotype analysis of Latilactobacills curvatus from different niches: Carbohydrate metabolism, antibiotic resistance, bacteriocin, phage fragments and linkages with CRISPR-Cas systems

The potential probiotic function of Latilactobacills curvatus has attracted the attention of researchers. To explore the differences in the genomes of L. curvatus, nine strains were isolated from various sources, including feces and fermented vegetables and compared with 25 strains from the NCBI database. The findings indicated that the average genome size, GC content, and CDS of L. curvatus were 1.94 MB, 41.9%, and 1825, respectively. Its core genome is associated with transcription, translation, carbohydrate transport and metabolism, and defense functions. The pan-genome of L. curvatus was in a closed state. The genetic diversity of L. curatus is mainly manifested in its ability to use carbohydrates, antibiotic resistance, bacteriocin operon, and polymeric regularly interspaced short palindromic repeats (CRISPR)-Cas for bacterial immunity. The CRISPR system of 34 strains of L. curvatus was predominantly found to be of the IIA type with a few IIC and IE types. These findings will contribute to a better understanding of this species.

Lactation time influences the composition of Bifidobacterium and Lactobacillus at species level in human breast milk

Human breast milk is a source of microorganisms for infants that play an important role in building infant gut health and immunity. The bacterial composition in human breast milk is influenced by lactation time. This study aimed to investigate the influence of lactation time on bacteria in breast milk at the genus level and the species levels of Bifidobacterium and Lactobacillus on days 2-4, 8, 14, and 30. Eighteen individuals were recruited and 60 milk samples were collected. The 16S rRNA gene, and the bifidobacterial groEL and lactobacilli groEL genes were used for amplicon sequencing. The results revealed that the alpha diversities of colostrum and transition 1 (day 8) milk were lower than that of transition 2 (day 14) and mature milk. PCoA analysis showed that bacterial composition in colostrum and transition 1 milk differed from transition 2 and mature milk. A lower relative abundance of Blautia was found in colostrum and transition 1 milk compared with mature milk and lower abundances of Ruminococcus, Dorea, and Escherichia-Shigella were found in transition 1 compared with mature milk. Bifidobacterium ruminantium, Limosilactobacillus mucosae, and Ligilactobacillus ruminis were the predominant species across all four lactation stages, while Bifidobacterium bifidum was lower in transition 1, and Bifidobacterium pseudocatenulatum and Bifidobacterium pseudolongum were higher in transition 1 milk. This study indicated that the bacterial composition in colostrum was more similar to that of transition 1 milk, whereas the bacterial community in transition 2 milk was similar to that of mature milk which suggests that bacterial composition in human breast milk shows stage-specific signatures even within a short period at both genus level and Bifidobacterium and Lactobacillus species levels, providing insights into probiotic supplementation for the nursing mother.

Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways

(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.

Mechanism of gastrointestinal adaptability and antioxidant function of infant-derived Lactobacillus plantarum BF_15 through genomics

Lactobacillus plantarum is an essential probiotic in the human gastrointestinal tract. L. plantarum BF_15, a functional probiotic isolated from the feces of breast-fed infants, has been reported in many in vitro and in vivo studies with strong gastrointestinal adaptability and outstanding anti-oxidative activities. Therefore, the whole genome of L. plantarum BF_15 was sequenced. Several genes, encoding the gastrointestinal adaptability-related proteins, were identified, including genes related to gastrointestinal environment-induced stress resistance, adhesive performance, and ability to transport and metabolize resistant starch and oligosaccharides. Genes related to alleviating oxidative stress were also found. Further functional verification was carried out by RT-qPCR on the 10 and 12 key adhesion and antioxidant genes. Overall, this study might provide a critical basis for L. plantarum BF_15 as a potential candidate for probiotics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01132-w.

Genomic diversity of genus Limosilactobacillus

The genus Limosilactobacillus (formerly Lactobacillus) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed comparative genomic analysis of Limosilactobacillus (22 species; 332 genomes) isolated from different niches, further focusing on human strains (11 species; 74 genomes) and their adaptation features to specific body sites. Phylogenomic analysis of Limosilactobacillus showed misidentification of some strains deposited in public databases and existence of putative novel Limosilactobacillus species. The pangenome analysis revealed a remarkable genomic diversity (only 1.3 % of gene clusters are shared), and we did not observe a strong association of the accessory genome with different niches. The pangenome of Limosilactobacillus reuteri and Limosilactobacillus fermentum was open, suggesting that acquisition of genes is still occurring. Although most Limosilactobacillus were predicted as antibiotic susceptible (83%), acquired antibiotic-resistance genes were common in L. reuteri from food-producing animals. Genes related to lactic acid isoform production (>95 %) and putative bacteriocins (70.2%) were identified in most Limosilactobacillus strains, while prophages (55.4%) and CRISPR-Cas systems (32.0%) were less prevalent. Among strains from human sources, several metabolic pathways were predicted as conserved and completed. Their accessory genome was highly variable and did not cluster according to different human body sites, with some exceptions (urogenital Limosilactobacillus vaginalis, Limosilactobacillus portuensis, Limosilactobacillus urinaemulieris and Limosilactobacillus coleohominis or gastrointestinal Limosilactobacillus mucosae). Moreover, we identified 12 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues that were significantly enriched in strains from particular body sites. We concluded that evolution of the highly diverse Limosilactobacillus is complex and not always related to niche or human body site origin.

Immunomodulatory potential of four candidate probiotic Lactobacillus strains from plant and animal origin using comparative genomic analysis

Probiotic strains from different origins have shown promise in recent decades for their health benefits, for example in promoting and regulating the immune system. The immunomodulatory potential of four Lactobacillus strains from animal and plant origins was evaluated in this paper based on their genomic information. Comparative genomic analysis was performed through genome alignment, average nucleotide identity (ANI) analysis and gene mining for putative immunomodulatory genes. The genomes of the four Lactobacillus strains show relative similarities in multiple regions, as observed in the genome alignment. However, ANI analysis showed that L. mucosae LM1 and L. fermentum SK152 are the most similar when considering their nucleotide sequences alone. Gene mining of putative immunomodulatory genes studied from L. plantarum WCFS1 yielded multiple results in the four potential probiotic strains, with L. plantarum SK151 showing the largest number of genes at around 74 hits, followed by L. johnsonii PF01 at 41 genes when adjusted for matches with at least 30 % identity. Looking at the immunomodulatory genes in each strain, L. plantarum SK151 and L. johnsonii PF01 may have wider activity, covering both immune activation and immune suppression, as compared to L. mucosae LM1 and L. fermentum SK152, which could be more effective in activating immune cells and the pro-inflammatory cascade rather than suppressing it. The similarities and differences between the four Lactobacillus species showed that there is no definitive trend based on the origin of isolation alone. Moreover, higher percentage identities between genomes do not directly correlate with higher similarities in potential activity, such as in immunomodulation. The immunomodulatory function of each of the four Lactobacillus strains should be observed and verified experimentally in the future, since some the activity of some genes may be strain-specific, which would not be identified through comparative genomics alone.

Exploring the Bile Stress Response of Lactobacillus mucosae LM1 through Exoproteome Analysis

Lactobacillus sp. have long been studied for their great potential in probiotic applications. Recently, proteomics analysis has become a useful tool for studies on potential lactobacilli probiotics. Specifically, proteomics has helped determine and describe the physiological changes that lactic acid bacteria undergo in specific conditions, especially in the host gut. In particular, the extracellular proteome, or exoproteome, of lactobacilli contains proteins specific to host– or environment–microbe interactions. Using gel-free, label-free ultra-high performance liquid chromatography tandem mass spectrometry, we explored the exoproteome of the probiotic candidate Lactobacillus mucosae LM1 subjected to bile treatment, to determine the proteins it may use against bile stress in the gut. Bile stress increased the size of the LM1 exoproteome, secreting ribosomal proteins (50S ribosomal protein L27 and L16) and metabolic proteins (lactate dehydrogenase, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate dehydrogenases, among others) that might have moonlighting functions in the LM1 bile stress response. Interestingly, membrane-associated proteins (transporters, peptidase, ligase and cell division protein ftsH) were among the key proteins whose secretion were induced by the LM1 bile stress response. These specific proteins from LM1 exoproteome will be useful in observing the proposed bile response mechanisms via in vitro experiments. Our data also reveal the possible beneficial effects of LM1 to the host gut.

Mixed Acid Fermentation of Carbohydrate-Rich Dairy Manure Hydrolysate

Dairy manure (DM) is an abundant agricultural residue that is largely composed of lignocellulosic biomass. The aim of this study was to investigate if carbon derived from DM fibers can be recovered as medium-chain fatty acids (MCFAs), which are mixed culture fermentation products of economic interest. DM fibers were subjected to combinations of physical, enzymatic, chemical, and thermochemical pretreatments to evaluate the possibility of producing carbohydrate-rich hydrolysates suitable for microbial fermentation by mixed cultures. Among the pretreatments tested, decrystalization dilute acid pretreatment (DCDA) produced the highest concentrations of glucose and xylose, and was selected for further experiments. Bioreactors fed DCDA hydrolysate were operated. Acetic acid and butyric acid comprised the majority of end products during operation of the bioreactors. MCFAs were transiently produced at a maximum concentration of 0.17 mg COD_MCFAs/mg COD_Total. Analyses of the microbial communities in the bioreactors suggest that lactic acid bacteria, Megasphaera, and Caproiciproducens were involved in MCFA and C4 production during DCDA hydrolysate metabolism.

Synergistic interactions prevail in multispecies biofilms formed by the human gut microbiota on mucin

Bacterial species in the human gut predominantly exist in the form of mixed-species biofilms on mucosal surfaces. In this study, the biofilm-forming ability of many human gut bacterial strains (133 strains recovered from human faeces) on mucin-coated and non-coated polystyrene surfaces was determined. A significant variation (P < 0.05) in the biofilm-forming ability of many bacterial species on both surfaces was noticed. Based on some preliminary trials, four bacterial species were selected (Bifidobacterium bifidum, Bifidobacterium longum subsp. infantis, Parabacteroides distasonis and Bacteroides ovatus), which could not form any abundant biofilm individually under the in vitro conditions investigated, but produced abundant biofilms when co-cultured in different combinations of two, three and four species, giving an evidence of synergistic interactions in multispecies biofilm formation. There was a 4.74-fold increase in the biofilm mass when all strains developed a biofilm together. Strain-specific qPCR analysis showed that B. bifidum was the most dominant species (56%) in the four-species biofilm after 24 h, followed by B. longum subsp. infantis (36.2%). Study involving cell free supernatant of the cooperating strains showed that cell viability as well as physical presence of cooperating cells were prerequisites for the observed synergy in biofilms. The molecular mechanism behind these interactions and subsequent effects on the functionality of the strains involved were not determined in our study but merit further work.

Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches

Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L.&nbsp;sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L.&nbsp;sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L.&nbsp;sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.

Complete genome sequence of Lactobacillus plantarum SK156, a candidate vehicle for mucosal vaccine delivery

Lactobacillus plantarum SK156 was isolated from traditional Korean food. The genome of SK156 strain consists of a circular chromosome (3,231,383 bp) with guanine (G) + cytosine (C) content of 44.56%. Among the predicted 2,991 protein-coding genes, the genome included genes encoding for α-amylase, which hydrolyzes α-bonds of polysaccharides. Genomic sequencing of L. plantarum SK156 will give information on the mechanism involved in the enzymatic degradation of polysaccharides and its application for improving feed efficiency.

Proteomic Analysis Identifies Dysregulated Proteins in Butanol-Tolerant Gram-Positive Lactobacillus mucosae BR0713-33

Butanol can be produced biologically through fermentation of lignocellulosic biomass-derived sugars by Gram-positive Clostridium species. For cost-effective production, increased butanol fermentation titers are desired. However, the currently available butanol-fermenting microbes do not tolerate sufficiently high butanol concentrations; thus, new butanol-tolerant strains are desired. One promising strategy is to genetically modify Clostridium species by introducing stress tolerance-associated genes. This study was aimed to seek butanol tolerance genes from other Gram-positive species, which might be better suited than those from Gram-negative E. coli or eukaryotic Saccharomyces cerevisiae. Several butanol-tolerant lactobacilli were reported previously, and Lactobacillus mucosae BR0713-33, which showed the most robust anaerobic growth in 4% butanol, was used here for proteomics analyses. Cellular proteins that responded to 2, 3, and 4% butanol were characterized. Twenty-nine proteins that were identified were dysregulated in response to increased concentrations of butanol in L. mucosae . Seventeen genes involved in coding for stress-tolerant proteins GroES, GroEL, and DnaK and genes involved in substrate utilization, fatty acid metabolism, and nucleotide synthesis were induced by increased butanol, and 12 genes involving energy production (F₀F₁ATP synthases) and redox balance preservation were repressed by increased butanol. These results can help guide targeted engineering strategies to improve tolerance and production of biobutanol.

Niche-Specific Adaptive Evolution of Lactobacillus plantarum Strains Isolated From Human Feces and Paocai

Lactobacillus plantarum, a widely used probiotic in the food industry, exists in diverse habitats, which has led to its niche-specific genetic evolution. However, the relationship between this type of genetic evolution and the bacterial phenotype remains unclear. Here, six L. plantarum strains derived from paocai and human feces were analyzed at the genomic and phenotypic levels to investigate the features of adaptive evolution in different habitats. A comparative genomic analysis showed that 93 metabolism-related genes underwent structural variations (SVs) during adaptive evolution, including genes responsible for carbohydrate, lipid, amino acid, inorganic ion and coenzyme transport and metabolism, and energy production and conversion. Notably, seven virulence factor-related genes in strains from both habitats showed SVs — similar to the pattern found in the orthologous virulence genes of pathogenic bacteria shared similar niches, suggesting the possibility of horizontal gene transfer. These genomic variations further influenced the metabolic abilities of strains and their interactions with the commensal microbiota in the host intestine. Compared with the strains from feces, those from paocai exhibited a shorter stagnation period and a higher growth rate in a diluted paocai solution because of variations in functional genes. In addition, opposite correlations were identified between the relative abundances of L. plantarum strains and the genus Bifidobacterium in two media inoculated with strains from the two habitats. Overall, our findings revealed that the niche-specific genetic evolution of L. plantarum strains is associated with their fermentation abilities and physiological functions in host gut health. This knowledge can help guiding the exploration and application of probiotics from the specific niches-based probiotic exploitation.

The Composition and Concordance of Lactobacillus Populations of Infant Gut and the Corresponding Breast-Milk and Maternal Gut

The maternal gut is the principal source of commensal bacteria in the infant gut during the lactation stage, where breast milk acts as an intermediary for the transfer of potential probiotic bacteria consortia, including Lactobacillus. This study aimed to characterize the bacterial communities in human milk, maternal, and infant feces in a small yet very homogeneous cohort of 25 healthy mother–infant pairs in northwestern China (n = 25, infant age from 7 days to 2 years), with special emphasis on the cooccurrence and vertical transfer of Lactobacillus phylotypes at the species or strain level in mother-breast milk-infant triads. Accurate sequencing analysis revealed that among 73 Lactobacillus zero-radius operational classification units (ZOTUs) identified, 58 belonging to 18 recognized species or species groups were distributed in all three types of samples. Lactobacillus ruminis, L. mucosae and L. gasseri-johnsonii as true residents were the most represented in all three ecosystems, whereas the content of Lactobacillus phylotypes commonly developed as probiotics was not dominant. While the numbers of Lactobacillus species in breast milk and infant feces were greater than that in maternal feces, principal coordinates analysis (PCoA) based on beta diversity, coupled with the frequency of isolates determined by culture methods, showed that the Lactobacillus community in the infant gut was more similar to that in the maternal gut than to that in breast milk, suggesting that the gut is niche selective for Lactobacillus populations. In addition, identical strains of L. ruminis, L. paracasei, L. mucosae and L. salivarius were isolated from multiple mother–infant pairs, supporting the hypothesis that vertical transfer of bacteria via breastfeeding contributes to the initial establishment of the microbiota in the developing infant intestine.

Complete genome sequence of the acidic cellulase producer Bacillus amyloliquefaciens ATC6

Here we report the complete genome sequence of Bacillus amyloliquefaciens ATC6, which produces acidic cellulase, isolated from pig feces. The genome is 4,062,817 bp in length and has a guanine-cytosine (GC) content of 46.27%. Among the predicted 3,913 protein-coding genes, two glucanase genes, which are involved in lichenan and cellulose degradation, were found. This genome analysis helps clarify the mechanism involved in cellulose biodegradation and support its application for efficient use of livestock feeds.

Characterisation of a lysophospholipase from Lactobacillus mucosae

OBJECTIVE

In this study, we characterised a novel lysophospholipase (LysoPL) from the L. mucosae LM1 strain. The gene, LM-lysoPL, encoding LysoPL from L. mucosae LM1 was cloned, analyzed, and expressed.

RESULTS

LM-lysoPL contained a conserved region and catalytic triad motif responsible for lysophospholipase activity. After purification, UHPLC-MS analysis showed that recombinant LM-LysoPL hydrolyzed phosphatidic acid, generating lysophosphatidic acid. The enzyme had greater hydrolytic activity against C16 and C18 fatty acids, indicating a preference for long-chain fatty acids. Enzymatic assays showed that the optimal pH and temperature of recombinant LM-LysoPL were 7 and 30 °C, respectively, and it was enzymatically active within a narrow pH range.

CONCLUSIONS

To the best of our knowledge, this is the first study to identify and characterize a lysophospholipase from lactic acid bacteria. Our findings provide a basis for understanding the probiotic role of L. mucosae LM1 in the gut.

Comparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System

Pediococcus pentosaceus isolated from fermented food and the gastrointestinal tracts of humans and animals have been widely identified, and some strains have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, the genomes of 65 P. pentosaceus strains isolated from human and animal feces and different fermented food were sequenced and comparative genomics analysis was performed on all strains along with nine sequenced representative strains to preliminarily reveal the lifestyle of P. pentosaceus, and investigate the genomic diversity within this species. The results reveal that P. pentosaceus is not host-specific, and shares core genes encoding proteins related to translation, ribosomal structure and biogenesis and signal transduction mechanisms, while its genetic diversity relates mainly to carbohydrate metabolism, and horizontally transferred DNA, especially prophages and bacteriocins encoded on plasmids. Additionally, this is the first report of a type IIA CRISPR/Cas system in P. pentosaceus. This work provides expanded resources of P. pentosaceus genomes, and offers a framework for understanding the biotechnological potential of this species.

Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches

The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of L. mucosae mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of L. mucosae mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among L. mucosae. Additionally, the type IIIA CRISPR-Cas system was discovered in L. mucosae for the first time. This work provided new ideas for the study of this species.

Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.

Genetic and Biochemical Characterization of an Exopolysaccharide With in vitro Antitumoral Activity Produced by Lactobacillus fermentum YL-11

In the present study, the whole genome sequence of Lactobacillus fermentum YL-11, a novel exopolysaccharide (EPS)-producing lactic acid bacteria (LAB) strain isolated from fermented milk, was determined. Genetic information and the synthetic mechanism of the EPS in L. fermentum YL-11 were identified based on bioinformatic analysis of the complete genome. The purified EPS of YL-11 mainly comprised galactose (48.0%), glucose (30.3%), mannose (11.8%), and arabinose (6.0%). In vitro, the EPS from YL-11 exhibited inhibition activity against HT-29 and Caco-2 colon cancer cells, suggesting that EPS from strain YL-11 might be used as an antitumoral agent. EPS at 600 and 800 μg/mL achieved inhibition rates of 46.5 ± 3.5% and 45.6 ± 6.1% to HT-29 cells, respectively. The genomic information about L. fermentum YL-11 and the antitumoral activity of YL-11 EPS provide a theoretical foundation for the future application of EPS in the food and pharmaceutical industries.

Bifidobacterium and Lactobacillus Composition at Species Level and Gut Microbiota Diversity in Infants before 6 Weeks

Our objective was to investigate the effects of different delivery and feeding modes on the gut microbiota composition of early infants with special emphasis on Bifidobacterium and Lactobacillus profiles at species level. 16S rRNA V3-V4 regions, bifidobacterial, and lactobacilli groEL genes from infant feces were sequenced by Illumina MiSeq. Gut microbiota abundance was significantly different, where standard vaginally delivered (SVD) and breast-fed (BF) groups were higher in comparison with caesarean section (CS), milk-powder-fed (MPF), and mixed-fed (MF) groups. The genus unclassified Enterobacteriaceae was dominant, followed by Bifidobacterium, which was highly abundant in SVD and BF groups. The dominant Bifidobacterium species in all groups were B. longum subsp. longum, B. longum subsp. infantis and B. animalis subsp. lactis. B. dentium and the diversity of Bifidobacterium in SVD and BF groups were significantly higher. For Lactobacillus profiles, L. rhamnosus and L. gasseri were dominant among all the groups, while Lactobacillus species in CS and MPF groups were more diverse. Functional predictions showed significant differences between delivery mode and feeding groups, such as phosphotransferase system as well as taurine and hypotaurine metabolism. In early infants with different delivery and feeding methods, gut microbiota-particularly bifidobacteria and lactobacilli communities-showed significant differences, with strong implications for physiological functions.