The genus Lactobacillus--a genomic basis for understanding its diversity

Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice

BACKGROUND

Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in colitis remains largely unexplored.

RESULTS

In this study, we isolated bacteria from fecal samples of a healthy donor and a patient with ulcerative colitis in remission. Subsequently, we identified three bacterial strains that exhibited a notable ability to ameliorate dextran sulfate sodium (DSS)-induced colitis, as evidenced by increased colon length, reduced disease activity index, and improved histological score. Further analysis revealed that each of Pediococcus acidilactici CGMCC NO.17,943, Enterococcus faecium CGMCC NO.17,944 and Escherichia coli CGMCC NO.17,945 significantly attenuated inflammatory responses and restored gut barrier dysfunction in mice. Mechanistically, bacterial 16S rRNA gene sequencing indicated that these three strains partially restored the overall structure of the gut microbiota disrupted by DSS. Specially, they promoted the growth of Faecalibaculum and Lactobacillus murinus, which were positively correlated with gut barrier function, while suppressing Odoribacter, Rikenella, Oscillibacter and Parasutterella, which were related to inflammation. Additionally, these strains modulated the composition of short chain fatty acids (SCFAs) in the cecal content, leading to an increase in acetate and a decrease in butyrate. Furthermore, the expression of metabolites related receptors, such as receptor G Protein-coupled receptor (GPR) 43, were also affected. Notably, the depletion of endogenous gut microbiota using broad-spectrum antibiotics completely abrogated these protective effects.

CONCLUSIONS

Our findings suggest that selected human-derived bacterial strains alleviate experimental colitis and intestinal barrier dysfunction through mediating resident gut microbiota and their metabolites in mice. This study provides valuable insights into the potential therapeutic application of probiotics in the treatment of colitis.

Research progress of targeted therapy regulating Th17/Treg balance in bone immune diseases

Rheumatoid arthritis (RA) and postmenopausal osteoporosis (PMOP) are common bone-immune diseases. The imbalance between helper (Th17) and regulatory T cells (Tregs) produced during differentiation of CD4+ T cells plays a key regulatory role in bone remodelling disorders in RA and PMOP. However, the specific regulatory mechanism of this imbalance in bone remodelling in RA and PMOP has not been clarified. Identifying the regulatory mechanism underlying the Th17/Treg imbalance in RA and PMOP during bone remodelling represents a key factor in the research and development of new drugs for bone immune diseases. In this review, the potential roles of Th17, Treg, and Th17/Treg imbalance in regulating bone remodelling in RA and PMOP have been summarised, and the potential mechanisms by which probiotics, traditional Chinese medicine compounds, and monomers maintain bone remodelling by regulating the Th17/Treg balance are expounded. The maintenance of Th17/Treg balance could be considered as an therapeutic alternative for the treatment of RA and PMOP. This study also summarizes the advantages and disadvantages of conventional treatments and the quality of life and rehabilitation of patients with RA and PMOP. The findings presented her will provide a better understanding of the close relationship between bone immunity and bone remodelling in chronic bone diseases and new ideas for future research, prevention, and treatment of bone immune diseases.

Taxonomy, Sequence Variance and Functional Profiling of the Microbial Community of Long-Ripened Cheddar Cheese Using Shotgun Metagenomics

Shotgun metagenomic sequencing was used to investigate the diversity of the microbial community of Cheddar cheese ripened over 32 months. The changes in taxa abundance were compared from assembly-based, non-assembly-based, and mOTUs2 sequencing pipelines to delineate the community profile for each age group. Metagenomic assembled genomes (MAGs) passing the quality threshold were obtained for 11 species from 58 samples. Although Lactococcus cremoris and Lacticaseibacillus paracasei were dominant across the shotgun samples, other species were identified using MG-RAST. NMDS analysis of the beta diversity of the microbial community revealed the similarity of the cheeses in older age groups (7 months to 32 months). As expected, the abundance of Lactococcus cremoris consistently decreased over ripening, while the proportion of permeable cells increased. Over the ripening period, the relative abundance of viable Lacticaseibacillus paracasei progressively increased, but at a variable rate among trials. Reads attributed to Siphoviridae and Ascomycota remained below 1% relative abundance. The functional profiles of PMA-treated cheeses differed from those of non-PMA-treated cheeses. Starter rotation was reflected in the single nucleotide variant profiles of Lactococcus cremoris (SNVs of this species using mOTUs2), while the incoming milk was the leading factor in discriminating Lacticaseibacillus paracasei/casei SNV profiles. The relative abundance estimates from Kraken2, non-assembly-based (MG-RAST) and marker gene clusters (mOTUs2) were consistent across age groups for the two dominant taxa. Metagenomics enabled sequence variant analysis below the bacterial species level and functional profiling that may affect the metabolic interactions between subpopulations in cheese during ripening, which could help explain the overall flavour development of cheese. Future work will integrate microbial variants with volatile profiles to associate the development of compounds related to cheese flavour at each ripening stage.

Application of 16S rRNA virtual RFLP for the discrimination of some closely taxonomic-related lactobacilli species

BACKGROUND

Several species in Lactobacillaceae family were recognized as potential probiotic bacteria. In this group of lactic acid bacteria, species are taxonomically closed and usually share similar 16S rRNA gene, thus, instead of so their identification and discrimination are too difficult.

METHOD

In the present study, virtual restriction fragment length polymorphism (RFLP) is instead of was used as a tool to discriminate between the closely related species Lactiplantibacillus plantarum (L plantarum), Lactiplantibacillus paraplantarum (L paraplantarum), and Lactiplantibacillus pentosus (L pentosus); Latilactobacillus sakei (L sakei), Latilactobacillus curvatus(L curvatus), and Latilactobacillus graminis (L graminis); Lacticaseibacillus casei (L casei), Lacticaseibacillus paracasei (L paracasei), Lacticaseibacillus zeae, and Lacticaseibacillus rhamnosus; Lactobacillus gasseri (L gasseri) and Lactobacillus johnsonii (L johnsonii). In silico comparative analysis of 16S rRNA sequences digested by 280 restriction enzymes was performed in order to search the key enzymes which gives different profiles.

RESULTS

Results revealed that L casei, L paracasei, L zeae, and Lb rhamnosus could be separated from each other on the basis of AlwI, BpuEI, BsgI, BsrDI, BstYI, EarI, MluCI, and NsPI RFLP. Results showed also that different RFLP patterns were obtained from L sakei, L graminis and L curvatus by using both AflI and NspI endonucleases (in separated restriction) and L plantarum, L paraplantarum, and L pentosus were distinguished each one from the other by MucI, NspI, and TspDTI PCR-RFLP. Lb gasseri and L johnsonii were also separated on the basis of Mse I, Taq I, and Dra I RFLP.

CONCLUSION

In this study, we proved that too closely related species could be separated in virtual analysis on basis of their 16S rRNA RFLP patterns using key restriction enzymes method.

Effect of adding probiotics to an antibiotic intervention on the human gut microbial diversity and composition: a systematic review

Introduction. Millions of antibiotic prescriptions are written annually in the USA.

Gap Statement. Probiotics reduce antibiotic-induced gastrointestinal side effects; however, the effect of probiotics on preserving gut microbial composition in response to antibiotics is not well understood.

Aim. To evaluate whether the addition of probiotics is capable of reverting the changes in alpha diversity and gut microbial composition commonly observed in adult participants receiving antibiotics.

Methodology. A search was conducted by two researchers following the PRISMA guidelines using PubMed, Science Direct, Cochrane and Embase from January to December 2021 with the following inclusion criteria: (i) randomized clinical trials assessing the effect of antibiotics, probiotics or antibiotics+probiotics; (ii) 16S rRNA; (iii) adult participants; and (iv) in English. Once data was extracted in tables, a third researcher compared, evaluated and merged the collected data. The National Institutes of Health (NIH) rating system was utilized to analyse risk of bias.

Results. A total of 29 articles (n=11 antibiotics, n=11 probiotics and n=7 antibiotics+probiotics) met the inclusion criteria. The lack of standardization of protocols to analyse the gut microbial composition and the wide range of selected antibiotics/probiotics complicated data interpretation; however, despite these discrepancies, probiotic co-administration with antibiotics seemed to prevent some, but not all, of the gut microbial diversity and composition changes induced by antibiotics, including restoration of health-related bacteria such as Faecalibacterium prausnitzii .

Conclusion. Addition of probiotics to antibiotic interventions seems to preserve alpha diversity and ameliorate the changes to gut microbial composition caused by antibiotic interventions.

The Functional Roles of Lactobacillus acidophilus in Different Physiological and Pathological Processes

Probiotics are live microorganisms that can be consumed by humans in amounts sufficient to offer health-promoting effects. Owing to their various biological functions, probiotics are widely used in biological engineering, industry and agriculture, food safety, and the life and health fields. Lactobacillus acidophilus (L. acidophilus), an important human intestinal probiotic, was originally isolated from the human gastrointestinal tract and its functions have been widely studied ever since it was named in 1900. L. acidophilus has been found to play important roles in many aspects of human health. Due to its good resistance against acid and bile salts, it has broad application prospects in functional, edible probiotic preparations. In this review, we explore the basic characteristics and biological functions of L. acidophilus based on the research progress made thus far worldwide. Various problems to be solved regarding the applications of probiotic products and their future development are also discussed.

Neonatal Morphine Results in Long-Lasting Alterations to the Gut Microbiome in Adolescence and Adulthood in a Murine Model

Despite the many advancements in the field of pain management, the use of intravenous opioids, such as morphine, in neonates is still a challenge for clinicians and researchers, as the available evidence concerning the long-term consequences of such an early exposure is limited. In particular, little is known concerning the long-term consequences of neonatal morphine exposure on the gut microbiome, which has been identified as a key modulator of health and diseases. Consequently, the purpose of this study was to investigate those long-term consequences of neonatal morphine on the gut microbiome. Newborn mice were exposed to either morphine (5 mg/kg/day) or saline for a duration of 7 ± 2 days. Fecal samples were collected during adolescence and adulthood to longitudinally assess the gut microbiome. DNA extracted from the stool samples were sent out for 16s rRNA sequencing. During adolescence, neonatal morphine resulted in a significant increase of α-diversity and an overall decrease in the abundance of several commensal genera. During adulthood, β-diversity revealed a significantly different microbial composition of the neonatally morphine-exposed mice than that of the controls. The results demonstrate that morphine exposure during this critical developmental period resulted in long-lasting changes, particularly a reduction in several commensal bacteria. Thus, an adjunct therapeutic intervention with probiotics could potentially be used along with opioids to manage pain while attenuating the long-term co-morbidities of neonatal morphine later in life.

Lactic Acid Bacteria in Raw-Milk Cheeses: From Starter Cultures to Probiotic Functions

Traditional cheeses produced from raw milk exhibit a complex microbiota, characterized by a sequence of different microorganisms from milk coagulation and throughout maturation. Lactic acid bacteria (LAB) play an essential role in traditional cheese making, either as starter cultures that cause the rapid acidification of milk or as secondary microbiota that play an important role during cheese ripening. The enzymes produced by such dynamic LAB communities in raw milk are crucial, since they support proteolysis and lipolysis as chief drivers of flavor and texture of cheese. Recently, several LAB species have been characterized and used as probiotics that successfully promote human health. This review highlights the latest trends encompassing LAB acting in traditional raw milk cheeses (from cow, sheep, and goat milk), and their potential as probiotics and producers of bioactive compounds with health-promoting effects.

Lactobacilli and human dental caries: more than mechanical retention

Lactobacilli have been considered as major contributors to human dental caries for over a century. Recent in vitro model studies have shown that when compared to Streptococcus mutans, a keystone pathogen of human dental caries, the ability of lactobacilli to form biofilms is poor, although differences exist between the different major species. Further studies using molecular and bioinformatics approaches provide evidence that multiple mechanisms, including adhesin-receptor mediated physical contact with S. mutans, facilitate the adherence and establishment of lactobacilli on the tooth surface. There is also evidence that under conditions like continuous sugar consumption, weak acids and other antimicrobials such as bacteriocins from lactobacilli can become detrimental to the microbial community, especially those in the proximity. Details on the underlying mechanisms of how different Lactobacillus sp. establish and persist in the highly complex microbiota on the tooth surface await further investigation.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Multi-product biorefinery from Arthrospira platensis biomass as feedstock for bioethanol and lactic acid production

With the aim to reach the maximum recovery of bulk and specialty bioproducts while minimizing waste generation, a multi-product biorefinery for ethanol and lactic acid production from the biomass of cyanobacterium Arthrospira platensis was investigated. Therefore, the residual biomass resulting from different pretreatments consisting of supercritical fluid extraction (SF) and microwave assisted extraction with non-polar (MN) and polar solvents (MP), previously applied on A. platensis to extract bioactive metabolites, was further valorized. In particular, it was used as a substrate for fermentation with Saccharomyces cerevisiae LPB-287 and Lactobacillus acidophilus ATCC 43121 to produce bioethanol (BE) and lactic acid (LA), respectively. The maximum concentrations achieved were 3.02 ± 0.07 g/L of BE by the MN process at 120 rpm 30 °C, and 9.67 ± 0.05 g/L of LA by the SF process at 120 rpm 37 °C. An economic analysis of BE and LA production was carried out to elucidate the impact of fermentation scale, fermenter costs, production titer, fermentation time and cyanobacterial biomass production cost. The results indicated that the critical variables are fermenter scale, equipment cost, and product titer; time process was analyzed but was not critical. As scale increased, costs tended to stabilize, but also more product was generated, which causes production costs per unit of product to sharply decrease. The median value of production cost was US$ 1.27 and US$ 0.39, for BE and LA, respectively, supporting the concept of cyanobacterium biomass being used for fermentation and subsequent extraction to obtain ethanol and lactic acid as end products from A. platensis.

Metabolomic evaluation of different starter culture effects on water-soluble and volatile compound profiles in nozawana pickle fermentation

Metabolomic characterization of a lactic-fermented pickle of nozawana (Brassica rapa L. var. hakabura) was conducted to evaluate the effects of different starter culture strains on the chemical profiles. We compared the profiles of water-soluble and volatile compounds obtained by non-targeted nuclear magnetic resonance and solid-phase microextraction gas chromatography/mass spectrometry analyses. Principal component analyses indicated that the fermented samples differed significantly in terms of the levels of various compounds, including taste- and aroma-active components, such as water-soluble residual sugars, organic acids, mannitol, ethanol, dihydroxyacetone, ornithine, γ-aminobutyric acid, choline, volatile isothiocyanates, 3,4-epithiobutyl cyanide, 2,3-butanedione, acetoin, ethyl acetate, dimethyl trisulfide, and S-methyl thioacetate. Fermentation with a Latilactobacillus curvatus culture was associated with a unique metabolite profile characterized by higher levels of isothiocyanates and hexanoic acid and lower levels of lactic acid, acetic acid, acetoin, and 2,3-butanedione. These variations in the chemical profile might be associated with different qualities in fermented nozawana pickle products.

A review on enzyme-producing lactobacilli associated with the human digestive process: From metabolism to application

Complex carbohydrates, proteins, and other food components require a longer digestion process to be absorbed by the lining of the alimentary canal. In addition to the enzymes of the gastrointestinal tract, gut microbiota, comprising a large range of bacteria and fungi, has complementary action on the production of digestive enzymes. Within this universe of "hidden soldiers", lactobacilli are extensively studied because of their ability to produce lactase, proteases, peptidases, fructanases, amylases, bile salt hydrolases, phytases, and esterases. The administration of living lactobacilli cells has been shown to increase nutrient digestibility. However, it is still little known how these microbial-derived enzymes act in the human body. Enzyme secretion may be affected by variations in temperature, pH, and other extreme conditions faced by the bacterial cells in the human body. Besides, lactobacilli administration cannot itself be considered the only factor interfering with enzyme secretion, human diet (microbial substrate) being determinant in their metabolism. This review highlights the potential of lactobacilli to release functional enzymes associated with the digestive process and how this complex metabolism can be explored to contribute to the human diet. Enzymatic activity of lactobacilli is exerted in a strain-dependent manner, i.e., within the same lactobacilli species, there are different enzyme contents, leading to a large variety of enzymatic activities. Thus, we report current methods to select the most promising lactobacilli strains as sources of bioactive enzymes. Finally, a patent landscape and commercial products are described to provide the state of art of the transfer of knowledge from the scientific sphere to the industrial application.

Influence of thermal assistance on the biodegradation of organics during food waste bio-drying: Microbial stimulation and energy assessment

Recently, bio-drying was highlighted in the drying pretreatment of high-moisture organic wastes for their energy recovery. In this study, to investigate the influences of thermal assistance on microbial stimulation and energy utilization in organic degradation, thermally assisted bio-drying (TB) was conducted on food waste (FW) and was compared with conventional bio-drying (CB) and thermal drying (TD). As expected, more water was removed in TB, which exhibited no lag phenomenon and intensified microbial activity. Corresponding with the stimulated enzyme activity, more readily degradable carbohydrates, lipids and lignocellulose were decomposed in TB than those in CB, and lipid degradation generated a significant proportion of the total bio-heat generated (43.13%-45.83%). Furthermore, according to the microbial analysis (qPCR and 16S rRNA gene sequencing), Bacillus was found to be the dominant genus involved in the degradation of organics during TB and CB. In the initial phase, rather than Weissella, as in CB, Ureibacillus was notable in TB for the degradation of readily degradable substrates. In the late phase, Pseudoxanthomonas and Saccharomonospora were enriched for degrading lignocellulose. In addition, heat balance and life-cycle energy assessment demonstrated that a small amount of thermal heat (11.96%) upgraded bio-drying with high energy efficiency. Compared with the CB and TD processes, the TB trial consumed less thermal energy (0.58 MJ/kg H₂O) and achieved a higher energy output/input ratio (3.64). This research suggests that thermal assistance is a promising approach to enhancing FW bio-drying, which exhibits efficient drying performance and great potential for energy recovery.

Introduction of Colonic and Fecal Microbiota From an Adult Pig Differently Affects the Growth, Gut Health, Intestinal Microbiota and Blood Metabolome of Newborn Piglets

Microbiota transplantation is a rapid and effective method for changing and reshaping the intestinal microbiota and metabolic profile in humans and animals. This study compared the different influences of the introduction of fecal microbes and colonic microbes from a fat, adult pig in newborn pigs. Both colonic microbiota transplantation (CMT) and fecal microbiota transplantation (FMT) promoted growth and improved gut functions in suckling pigs up to weaning. FMT was more beneficial for body weight gain and body fat deposition in piglets, while CMT was more beneficial for intestinal health and mucosal immunity. 16S rDNA sequence analysis indicated that both CMT and FMT significantly increased the abundances of beneficial or functional bacteria, such as Lactobacillus and Prevotella_2 genera, in the piglets, and reduced the abundances of harmful bacteria, such as Escherichia-Shigella. Blood metabolome analysis showed that transplantation, especially FMT, enhanced lipid metabolism in piglets. In addition, while CMT also changed amino acid metabolism and increased anti-inflammatory metabolites such as 3-indoleacetic acid and 3-indolepropionic acid in piglets, FMT did not. Of note, FMT damaged the intestinal barrier of piglets to a certain extent and increased the levels of inflammatory factors in the blood that are potentially harmful to the health of pigs. Taken together, these results suggested that intestinal and fecal microbiota transplantations elicited similar but different physiological effects on young animals, so the application of microbiota transplantation in animal production requires the careful selection and evaluation of source bacteria.

Draft genome sequence of Lactobacillus plantarum strain DMR17 isolated from homemade cow dahi of Sikkim Himalayan region: an evaluation of lactate fermentation and secondary metabolism

Lactobacillus plantarum DMR17 was isolated from homemade cow dahi of Sikkim Himalayan region of India. Here, we report the draft genome sequence of this strain. A total of 21,176,638 paired-end reads were obtained which were assembled into 65 contigs. The reference genome used was L. plantarum WCFS1. The genome size of DMR17 was 3,228,341 bp with G + C content of 46.25%. 3302 coding sequences were predicted including 68 tRNA and 67 rRNA genes. More than 88% of the total pre-processed reads from the sample were mapped to the reference genome. The identified coding proteins were classified into 27 functional categories based on COG classification. The genome was found to possess genes for lactate and mixed acid fermentation. The genome also showed the presence of genes for catabolism of aromatic compounds, phosphorous, and other metabolism. The genome information of L. plantarum DMR17 provides the basis for understanding the functional properties and to consider its use as a potential component of functional foods especially dahi.

The Prospective Beneficial Effects of Red Laser Exposure on Lactocaseibacillus casei Fermentation of Skim Milk

Probiotic lactic acid bacteria are crucial producers of fermented dairy products that are popular functional foods in many countries. The health benefits of probiotic bacteria are mainly attributed to their effective bioactive metabolites. The quality of fermented milk is mainly dependent on the bacterial strain used in the fermentation process. In this study, an innovative technique is used in order to enhance the activities of the probiotic bacteria, quality of fermented milk, and consequently the whole fermentation process. Red laser dosages, at the wavelength of 632.7 nm, were applied to the type strain Lacticaseibacillus casei NRRL-B-1922 before the fermentation of skim milk. The results revealed that the scavenging of 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) radical and total antioxidant capacity were significantly increased from 21% in untreated control to 56% after bacterial laser irradiation of 12 J/cm² dosage for 40 min. The antioxidant activity was found to be increased as the red laser dosage increased in a dose-response relationship. Additionally, the lactose fermentation in skim milk medium of 43.22 mg/mL initial concentration into organic acids was enhanced after L. casei irradiation and recorded 23.15 mg/mL compared to control group 28.35 mg/mL without bacterial pre-treatment. These results are correlated with increase of the β-Galactosidase activity, where the L. casei that has been exposed to 40 min of red laser exhibited the higher activity of a 0.37 unit/mL relative to the control 0.25 unit/mL. The assessment of this fermented milk after L. casei laser exposure for 10, 20, and 40 min indicates multiple biological effects, including assimilation of cholesterol as well as proteolytic and antibacterial activity. Our data on the exposure of L. casei to laser beam suggest promising application of red laser in the fermentation process of skim milk.

Probiotic low-fat fermented goat milk with passion fruit by-product: In vitro effect on obese individuals' microbiota and on metabolites production

This study aimed to evaluate the impact of a two-week treatment period with probiotic low-fat fermented goat milk by Lactobacillus casei Lc-1, supplemented with passion fruit by-product (1%), on the modulation of gut microbiota from obese individuals using the Simulator of Human Intestinal Microbial Ecosystem (SHIME) system. The effects were carried out through the study of gut microbiota composition, using 16S rRNA next generation sequencing, quantification of short-chain fatty acids (SCFA) and ammonium ions. The microbiota composition changed across three vessels representing the colon regions, because of fermented milk treatment. Fermented goat milk administration caused a reduction of bacteria belonging to genera Prevotella, Megamonas and Succinivibrio, which can produce SCFA, and an increase of Lactobacillus and Bifidobacterium genera in all simulated colon regions. There was no effect on SCFA and on ammonium ions concentration during treatment period. Fermented milk shifted the obese donors' microbiota without changing metabolites production. It happens, possibly, due to a balance in abundances among bacterial genera that can produce or not SCFA, and among bacterial genera with high or low proteolytic activity. Our outcomes help to clarify the effects of the ingestion of a probiotic low-fat fermented goat milk product on colon microbiota composition.

Lactobacillus enshiensis sp. nov., a novel arsenic-resistant bacterium

A lactic acid bacterial strain, HBUAS57009T, isolated from traditionally fermented food (Zha-Chili) in China, was characterized to clarify its taxonomic status using a polyphasic approach. Strain HBUAS57009T was phylogenetically closely related to Lactobacillus koreensis DCY50T, Lactobacillus fujinensis 218-6T, Lactobacillus mulengensis 112-3T, Lactobacillus cerevisiae TUM BP 140423000-2250T, Lactobacillus tongjiangensis 218-10T and Lactobacillus yonginensis THK-V8T with sequence similarities of 98.6–99.3 %. The genome-to-genome distance and average nucleotide identity values between the genomes of strain HBUAS57009T and type strains of closely related Lactobacillus species were less than 32.0 and 86.0 %, respectively; this is below the threshold for species boundaries. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1  ω9c and iso-C19 : 0. The G+C content of the genomic DNA of strain HBUAS57009T was 47.8 mol%. Examination of the functional categories of the genome revealed that strain HBUAS57009T could perform both homolactic and heterolactic fermentation processes to produce lactic acid via complete glycolysis and the pentose phosphate pathway. The putative biosynthesis pathway of butane-2,3-diol and acetoin, two important flavour compounds in the food industry, were identified using kegg mapper analysis. Based on its genotypic and phenotypic features, strain HBUAS57009T (=GDMCC 1.1664T=KACC 21424T) is designated as the type strain of a novel species, for which the name Lactobacillus enshiensis sp. nov. is proposed.

Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface

Bacterial surface-layers (S-layers) are crystalline arrays of repeating proteinaceous subunits that coat the exterior of many cell envelopes. S-layers have demonstrated diverse functions in growth and survival, maintenance of cell integrity, and mediation of host interactions. Additionally, S-layers can act as scaffolds for the outward display of auxiliary proteins and glycoproteins. These non-covalently bound S-layer associated proteins (SLAPs) have characterized roles in cell division, adherence to intestinal cells, and modulation of the host immune response. Recently, IgdA (LBA0695), a Lactobacillus acidophilus SLAP that possesses a Group 3 immunoglobulin (Ig)-like domain and GW (Gly-Tryp) dipeptide surface anchor, was recognized for its high conservation among S-layer-forming lactobacilli, constitutive expression, and surface localization. These findings prompted its selection for examination within the present study. Although IgdA and corresponding orthologs were shown to be unique to host-adapted lactobacilli, the Ig domain itself was specific to vertebrate-adapted species suggesting a role in vertebrate adaptation. Using a counterselective gene replacement system, igdA was deleted from the L. acidophilus NCFM chromosome. The resultant mutant, NCK2532, exhibited a visibly disrupted cell surface which likely contributed to its higher salt sensitivity, severely reduced adhesive capacity, and altered immunogenicity profile. Transcriptomic analyses revealed the induction of several stress response genes and secondary surface proteins. Due to the broad impact of IgdA on the cellular physiology and probiotic attributes of L. acidophilus, identification of similar proteins in alternative bacterial species may help pinpoint next-generation host-adapted probiotic candidates.

Comparison of eight Lactobacillus species for delivery of surface-displayed mycobacterial antigen

Lactobacillus spp. comprise a large group of Gram-positive lactic acid bacteria with varying physiological, ecological and immunomodulatory properties that are widely exploited by mankind, primarily in food production and as health-promoting probiotics. Recent years have shown increased interest in using lactobacilli for delivery of vaccines, mainly due to their ability to skew the immune system towards pro-inflammatory responses. We have compared the potential of eight Lactobacillus species, L. plantarum, L. brevis, L. curvatus, L. rhamnosus, L. sakei, L. gasseri, L. acidophilus and L. reuteri, as immunogenic carriers of the Ag85B-ESAT-6 antigen from Mycobacterium tuberculosis. Surface-display of the antigen was achieved in L. plantarum, L. brevis, L. gasseri and L. reuteri and these strains were further analyzed in terms of their in vitro and in vivo immunogenicity. All strains activated human dendritic cells in vitro. Immunization of mice using a homologous prime-boost regimen comprising a primary subcutaneous immunization followed by three intranasal boosters, led to slightly elevated IgG levels in serum in most strains, and, importantly, to significantly increased levels of antigen-specific mucosal IgA. Cellular immunity was assessed by studying antigen-specific T cell responses in splenocytes, which did not reveal proliferation as assessed by the expression of Ki67, but which showed clear antigen-specific IFN-γ and IL-17 responses for some of the groups. Taken together, the present results indicate that L. plantarum and L. brevis are the most promising carriers of TB vaccines.

Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain

Various Lactobacillus paracasei strains are found in diverse environments, including dairy and plant materials and the intestinal tract of humans and animals, and are also used in the food industry or as probiotics. In this study, we have isolated a new strain L. paracasei subsp. paracasei IBB3423 from samples of raw cow milk collected in a citizen science project. IBB3423 showed some desired probiotic features such as high adhesion capacity and ability to metabolize inulin. Its complete genome sequence comprising the chromosome of 3,183,386 bp and two plasmids of 5986 bp and 51,211 bp was determined. In silico analysis revealed numerous genes encoding proteins involved in carbohydrate metabolism and of extracellular localization likely supporting interaction with host tissues. In vitro tests confirmed the high adhesion capacity of IBB3423 and showed that it even exceeds that of the highly adhesive L. rhamnosus GG. Curing of the larger plasmid indicated that the adhesive properties depend on the plasmid and thus could be determined by its pilus-encoding spaCBA genes.

Exploiting Prophage-Mediated Lysis for Biotherapeutic Release by Lactobacillus reuteri

Lactobacillus reuteri has the potential to be developed as a microbial therapeutic delivery platform because of an established safety profile, health-promoting properties, and available genome editing tools. Here, we show that L. reuteri VPL1014 exhibits a low mutation rate compared to other Gram-positive bacteria, which we expect will contribute to the stability of genetically modified strains. VPL1014 encodes two biologically active prophages, which are induced during gastrointestinal transit. We hypothesized that intracellularly accumulated recombinant protein can be released following bacteriophage-mediated lysis. To test this, we engineered VPL1014 to accumulate leptin, our model protein, inside the cell. In vitro prophage induction of recombinant VPL1014 released leptin into the extracellular milieu, which corresponded to bacteriophage production. We also employed a plasmid system that does not require antibiotic in the growth medium for plasmid maintenance. Collectively, these data provide new avenues to exploit native prophages to deliver therapeutic molecules.IMPORTANCE Lactic acid bacteria (LAB) have been explored as potential biotherapeutic vehicles for the past 20 years. To secrete a therapeutic in the extracellular milieu, one typically relies on the bacterial secretion pathway, i.e., the Sec pathway. Overexpression of a secreted protein can overload the secretory pathway and impact the organism's fitness, and optimization of the signal peptide is also required to maximize the efficiency of the release of mature protein. Here, we describe a previously unexplored approach to release therapeutics from the probiotic Lactobacillus reuteri We demonstrate that an intracellularly accumulated recombinant protein is released following prophage activation. Since we recently demonstrated that prophages are activated during gastrointestinal transit, we propose that this method will provide a straightforward and efficient approach to deliver therapeutics in vivo.

The ameliorative effect of a Lactobacillus strain with good adhesion ability against dextran sulfate sodium-induced murine colitis

The objective of this study was to effectively screen out a Lactobacillus strain with excellent adhesion ability and ameliorative effect on the disease symptoms of a murine ulcerative colitis model.

Phenotypic Diversity of Lactobacillus sakei Strains

Lactobacillus sakei is a lactic acid bacteria (LAB) species highly adapted to the meat environment. For this reason, selected strains are often used as starter culture in the production of fermented sausages, especially in Mediterranean countries. It often represents the dominant species in these products and can maintain its viability during all the ripening period, which can take also some months. This ability is guaranteed by the possibility of the species to obtain energy through pathways active even when hexoses are depleted. This species is characterized by a relevant genetic and phenotypic diversity and its metabolism can be further affected by the growth condition applied. In this work we investigate the metabolic responses of six different L. sakei in a synthetic medium (DM) containing defined amounts of amino acids in relation to temperature and NaCl concentration. In addition, the activities of cells pre-grown in presence of glucose o ribose were tested. Arginine was efficiently up-taken with the exception of the type strain DSMZ 20017^t. Other amino acids (i.e., serine, asparagine, cysteine, and methionine) were metabolized through potentially energetic pathways which start from pyruvate accumulation, as demonstrated by the organic acid accumulation trend in the condition tested, especially in DM without sugar added. The presence of excesses of pyruvate deriving from amino acids lead to the accumulation of diacetyl and acetoin by all the strains when sugars were added. This approach allowed a deeper insight into the phenotypic variability of the species and improved the comprehension of the metabolic pathways adopted by L. sakei to survive and grow in restrictive conditions such as those found in fermented sausages during fermentations. Thus, the results obtained are useful information for improving and optimizing the use of such strains as starter culture for these products.

The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human

Glycoproteins are major players in the mucus protective barrier in the gastrointestinal and other mucosal surfaces. In particular the mucus glycoproteins, or mucins, are responsible for the protective gel barrier. They are characterized by their high carbohydrate content, present in their variable number, tandem repeat domains. Throughout evolution the mucins have been maintained as integral components of the mucosal barrier, emphasizing their essential biological status. The glycosylation of the mucins is achieved through a series of biosynthetic pathways processes, which generate the wide range of glycans found in these molecules. Thus mucins are decorated with molecules having information in the form of a glycocode. The enteric microbiota interacts with the mucosal mucus barrier in a variety of ways in order to fulfill its many normal processes. How bacteria read the glycocode and link to normal and pathological processes is outlined in the review.

Probiotic Lactobacillus Paracasei Expressing a Nucleic Acid-Hydrolyzing Minibody (3D8 Scfv) Enhances Probiotic Activities in Mice Intestine as Revealed by Metagenomic Analyses

Probiotics are well known for their beneficial effects for animals, including humans and livestock. Here, we tested the probiotic activity of Lactobacillus paracasei expressing 3D8 scFv, a nucleic acid-hydrolyzing mini-antibody, in mice intestine. A total of 18 fecal samples derived from three different conditions at two different time points were subjected to high-throughput 16S ribosomal RNA (rRNA) metagenomic analyses. Bioinformatic analyses identified an average of 290 operational taxonomic units. After administration of L. paracasei, populations of the probiotics L. paracasei, Lactobacillus reuteri, and Pediococcus acidilactici increased, whereas the population of harmful bacteria such as Helicobacter species decreased. Furthermore, continuous administration of L. paracasei resulted in L. paracasei emerging as the dominant probiotic after competition with other existing probiotics. Expression of 3D8 scFv protein specifically increased the population of P. acidilactici, which is another probiotic. In summary, our results showed that L. paracasei expressing 3D8 scFv protein enhanced probiotic activity in mice intestine with no observable side effects. Thus, the system developed in this study may be a good tool for the expression of recombinant protein using probiotics.

Gut Microbiome Composition in Non-human Primates Consuming a Western or Mediterranean Diet

The mammalian gastrointestinal tract harbors a highly diverse and dynamic community of bacteria. The array of this gut bacterial community, which functions collectively as a fully unified organ in the host metabolism, varies greatly among different host species and can be shaped by long-term nutritional interventions. Non-human primates, our close phylogenetic relatives and ancestors, provide an excellent model for studying diet-microbiome interaction; however, compared to clinical and rodent studies, research targeting primate gut microbiome has been limited. Herein, we analyze the gut microbiome composition in female cynomolgus macaques (Macaca fascicularis; n = 20) after the long-term (2.5 years) consumption of diets designed to mimic recent human Western- (WD; n = 10) or Mediterranean-type (MD; n = 10) diets. Microbiome diversity in MD consumers was significantly higher by the Shannon diversity index compared to the WD consumers, with similar but non-significant trends noted for the diversity metrics of species richness (Chao 1), observed operational taxonomic units (OTUs) and phylogenetic diversity (PD) whole Tree. Compared to the MD, the WD group demonstrated a higher Firmicutes-Bacteroides ratio and a significantly higher abundance of families Clostridiacea and Lactobacillaceae. Further analyses reveal significantly higher abundance of genera Lactobacillus, Clostridium, Faecalibacterium, and Oscillospira and lower abundance of Ruminococcus and Coprococcus in MD consumers relative to WD consumers. OTUs belonging to several species also show significant differences between the two groups, with Lactobacillus species demonstrating a prominently higher abundance in the MD consumers. The data reveal several differences in the gut microbiome of primates consuming the two different diets and should be useful for further studies aimed at understanding the diet-microbiome-health interactions in primates.

Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

Background

Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events.

Results

We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20′800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species’ level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class “genetic information processing” is conserved in the core-genome but that “signaling and cellular processes” is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation.

Conclusions

Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus’ evolution is directed by the environment and HGT.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4601-5) contains supplementary material, which is available to authorized users.

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level

Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus—to our knowledge—identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories “cell wall/membrane biogenesis” and “defense mechanisms” were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes. Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.

Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei

The lethal effects of soundwaves on a range of microorganisms have been known for almost a century whereas, the use of ultrasound to promote or control their activity is much more recent. Moreover, the fundamental molecular mechanism influencing the behaviour of microorganisms subjected to ultrasonic waves is not well established. In this study, we investigated the influence of ultrasonic frequencies of 20, 45, 130 and 950 kHz on growth kinetics of Lactobacillus sakei. A significant increase in the growth rate of L. sakei was observed following ultrasound treatment at 20 kHz despite the treatment yielding a significant reduction of ca. 3 log cfu/mL in cells count. Scanning electron microscopy showed that ultrasound caused significant changes on the cell surface of L. sakei culture with the formation of pores "sonoporation". Phenotypic microarrays showed that all ultrasound treated L. sakei after exposure to various carbon, nitrogen, phosphorus and sulphur sources had significant variations in nutrient utilisation. Integration of this phenotypic data with the genome of L. sakei revealed that various metabolic pathways were being influenced by the ultrasound treatments. Results presented in this study showed that the physiological response of L. sakei in response to US is frequency dependent and that it can influence metabolic pathways. Hence, ultrasound treatments can be employed to modulate microbial activity for specialised applications.

Genetic, enzymatic and metabolite profiling of the Lactobacillus casei group reveals strain biodiversity and potential applications for flavour diversification

AIMS

The Lactobacillus casei group represents a widely explored group of lactic acid bacteria, characterized by a high level of biodiversity. In this study, the genetic and phenotypic diversity of a collection of more than 300 isolates of the Lact. casei group and their potential to produce volatile metabolites important for flavour development in dairy products, was examined.

METHODS AND RESULTS

Following confirmation of species by 16S rRNA PCR, the diversity of the isolates was determined by pulsed-field gel electrophoresis. The activities of enzymes involved in the proteolytic cascade were assessed and significant differences among the strains were observed. Ten strains were chosen based on the results of their enzymes activities and they were analysed for their ability to produce volatiles in media with increased concentrations of a representative aromatic, branched chain and sulphur amino acid. Volatiles were assessed using gas chromatography coupled with mass spectrometry. Strain-dependent differences in the range and type of volatiles produced were evident.

CONCLUSIONS

Strains of the Lact. casei group are characterized by genetic and metabolic diversity which supports variability in volatile production.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a screening approach for the knowledge-based selection of strains potentially enabling flavour diversification in fermented dairy products.

Adhesion Properties of Lactic Acid Bacteria on Intestinal Mucin

Lactic acid bacteria (LAB) are Gram-positive bacteria that are natural inhabitants of the gastrointestinal (GI) tracts of mammals, including humans. Since Mechnikov first proposed that yogurt could prevent intestinal putrefaction and aging, the beneficial effects of LAB have been widely demonstrated. The region between the duodenum and the terminal of the ileum is the primary region colonized by LAB, particularly the Lactobacillus species, and this region is covered by a mucus layer composed mainly of mucin-type glycoproteins. The mucus layer plays a role in protecting the intestinal epithelial cells against damage, but is also considered to be critical for the adhesion of Lactobacillus in the GI tract. Consequently, the adhesion exhibited by lactobacilli on mucin has attracted attention as one of the critical factors contributing to the persistent beneficial effects of Lactobacillus in a constantly changing intestinal environment. Thus, understanding the interactions between Lactobacillus and mucin is crucial for elucidating the survival strategies of LAB in the GI tract. This review highlights the properties of the interactions between Lactobacillus and mucin, while concomitantly considering the structure of the GI tract from a histochemical perspective.

Draft Genome Sequence of Lactobacillus crispatus JCM5810, Which Can Reduce Campylobacter jejuni Colonization in Chicken Intestine

We present the 2.05-Mb draft genome sequence of Lactobacillus crispatus JCM5810, a chicken intestinal isolate with the ability to reduce Campylobacter jejuni colonization in chickens. The genome sequence will provide insights on the probiotic mechanisms of L. crispatus JCM5810.

Stress tolerance and physicochemical properties of encapsulation processes for Lactobacillus rhamnosus in pomegranate (Punica granatum L.) fruit juice

Encapsulation of Lactobacillus rhamnosus was performed using spray and freeze-drying. Maltodextrin and gum arabic were used in different combinations for spray-drying. Values of 50% maltodextrin and 40% gum arabic gave best results. Spray-drying was done at temperatures ranging from 110 to 150oC. Survivability, acid tolerance, antibiotic sensitivity testing, and total anthocyanin content and physical properties of moisture content, water activity, color analysis, bulk density, and tap density were analyzed. The moisture content of encapsulated powders ranged from 6.51 to 7.72% (wet basis) and bulk density and tap density values ranged from 0.334 to 0.308 g/cm³ and 0.350 to 0.330 g/cm³, respectively. Total anthocyanin contents were 19.28 and 7.264 mg/100 mL, respectively, for freeze and spray-dried powders. Freeze-dried probiotic pomegranate juice powder yielded best results with high survivability of Lactobacillus rhamnosus, a high total anthocyanin content, and other properties.

Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade

Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.

Prophage recombinases-mediated genome engineering in Lactobacillus plantarum

BACKGROUND

Lactobacillus plantarum is a food-grade microorganism with industrial and medical relevance belonging to the group of lactic acid bacteria (LAB). Traditional strategies for obtaining gene deletion variants in this organism are mainly vector-based double-crossover methods, which are inefficient and laborious. A feasible possibility to solve this problem is the recombineering, which greatly expands the possibilities for engineering DNA molecules in vivo in various organisms.

RESULTS

In this work, a double-stranded DNA (dsDNA) recombineering system was established in L. plantarum. An exonuclease encoded by lp_0642 and a potential host-nuclease inhibitor encoded by lp_0640 involved in dsDNA recombination were identified from a prophage P1 locus in L. plantarum WCFS1. These two proteins, combined with the previously characterized single strand annealing protein encoded by lp_0641, can perform homologous recombination between a heterologous dsDNA substrate and host genomic DNA. Based on this, we developed a method for marker-free genetic manipulation of the chromosome in L. plantarum.

CONCLUSIONS

This Lp_0640-41-42-mediated recombination allowed easy screening of mutants and could serve as an alternative to other genetic manipulation methods. We expect that this method can help for understanding the probiotic functionality and physiology of LAB.