Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification

Proteomic Analysis of Milk Fat Globule Membrane Protein Modulation of Differently Expressed Proteins in Lactobacillus plantarum under Bile Salt Stress

Tolerance to bile stress is a crucial property for lactic acid bacteria (LAB) to survive in the gastrointestinal tract and exert their beneficial effects. Whey powder enriched with milk fat globule membrane proteins (M-WPI) as a functional component is protective for strains under stress conditions. The current study investigated the key mechanisms of action involved in Lactobacillus plantarum (L. plantarum) CGMCC 23701 survival in the presence of bile and the protective mechanism of M-WPI. According to proteomic analysis (proteomics), there could be several reasons for the greater protective effect of M-WPI. These include promoting the synthesis of fatty acids and peptidoglycans to repair the structure of the cell surface, regulating the metabolism of carbohydrates and amino acids to release energy and produce a range of precursors, enabling the expression of the repair system to repair damaged DNA, and promoting the expression of proteins associated with the multidrug efflux pump, which facilitates the exocytosis of intracellular bile salts. This study helps us to better understand the changes in proteome of L. plantarum CGMCC 23701 under bile salt stress and M-WPI protection, which will provide a new method for the protection and development of functional LAB.

Comparative metatranscriptome analysis of Brazilian milk and water kefir beverages

The present study compared bacterial and fungal diversity of kefir beverages produced using milk (MK) or sugared water (WK) as propagation matrices and grains from the cities of Curitiba (CU) or Salvador (SA), Brazil, by sequencing the complete set of RNA transcripts produced in four products. In Brazil, milk and sugared water are used as matrices to propagate kefir grains. In all beverages, the bacterial community was composed of Lactobacillaceae and Acetobacteraceae. Saccharomycetaceae was the yeast family more abundant in WK, and Dipodascaceae and Pichiaceae in MK. Regarding KEGG mapping of functional orthologs, the four kefir samples shared 70% of KO entries of yeast genes but only 36% of bacterial genes. Concerning main metabolic processes, the relative abundance of transcripts associated with metabolism (energy metabolism) and environmental information processing (membrane transport) had the highest water/milk kefir ratio observed in Firmicutes. In contrast, transcripts associated with genetic information processing (protein translation, folding, sorting, and degradation) oppositely had the lowest water/milk ratios. Concluding, milk and water kefir have quite different communities of microorganisms. Still, the main mapped functional processes are similar, with only quantitative variation in membrane transport and energy acquisition in the water kefir and protein synthesis and turnover in the milk kefir.

Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols

Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.

Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid Fermented Shalgam Based on "In Silico" and "In Vitro" Approaches

This study aimed to characterize the genomic and metabolic properties of a novel Lb. fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called "shalgam." The genome size of AGA52 was 2,001,184 bp, which is predicted to carry 2024 genes, including 50 tRNAs, 3 rRNAs, 3 ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases, and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analyzed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsic originated. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Furthermore, the strain is found to have a better antioxidant capacity and to be tolerant to gastrointestinal simulated conditions. It was also observed that the AGA52 has antimicrobial activity against Yersinia enterocolitica ATCC9610, Bacillus cereus ATCC33019, Salmonella enterica sv. Typhimurium, Escherichia coli O157:h7 ATCC43897, Listeria monocytogenes ATCC7644, Klebsiella pneumoniae ATCC13883, and Proteus vulgaris ATCC8427. Additionally, AGA52 exhibited 42.74 ± 4.82% adherence to HT29 cells. Cholesterol assimilation (33.9 ± 0.005%) and GABA production capacities were also confirmed by "in silico" and "in vitro." Overall, the investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.

Mycobacteriales taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation

IMPORTANCE

A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order Mycobacteriales. Formal descriptions of proposed taxonomic changes based on our study are included.

An Overview of the Use and Applications of Limosilactobacillus fermentum in Broiler Chickens

The implementation of government regulations on antibiotic use, along with the public's concern for drug resistance, has strengthened interest in developing alternatives not only aimed at preserving animal production but also at reducing the effects of pathogenic infections. Probiotics, in particular, are considered microorganisms that induce health benefits in the host after consumption of adequate amounts; they have been established as a potential strategy for improving growth, especially by stimulating intestinal homeostasis. Probiotics are commonly associated with lactic acid bacteria, and Limosilactobacillus fermentum is a well-studied species recognized for its favorable characteristics, including adhesion to epithelial cells, production of antimicrobial compounds, and activation of receptors that prompt the transcription of immune-associated genes. Recently, this species has been used in animal production. Different studies have shown that the application of L. fermentum strains not only improves the intestinal ecosystem but also reduces the effects caused by potentially pathogenic microorganisms. These studies have also revealed key insights into the mechanisms behind the actions exerted by this probiotic. In this manuscript, we aim to provide a concise overview of the effects of L. fermentum administration on broiler chicken health and performance.

Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov

The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.

Administration of Ligilactobacillus salivarius CECT 30632 to elderly during the COVID-19 pandemic: Nasal and fecal metataxonomic analysis and fatty acid profiling

Elderly was the most affected population during the first COVID-19 and those living in nursing homes represented the most vulnerable group, with high mortality rates, until vaccines became available. In a previous article, we presented an open-label trial showing the beneficial effect of the strain Ligilactobacillus salivarius CECT 30632 (previously known as L. salivarius MP101) on the functional and nutritional status, and on the nasal and fecal inflammatory profiles of elderly residing in a nursing home highly affected by the pandemic. The objective of this post-hoc analysis was to elucidate if there were changes in the nasal and fecal bacteriomes of a subset of these patients as a result of the administration of the strain for 4 months and, also, its impact on their fecal fatty acids profiles. Culture-based methods showed that, while L. salivarius (species level) could not be detected in any of the fecal samples at day 0, L. salivarius CECT 30632 (strain level) was present in all the recruited people at day 120. Paradoxically, the increase in the L. salivarius counts was not reflected in changes in the metataxonomic analysis of the nasal and fecal samples or in changes in the fatty acid profiles in the fecal samples of the recruited people. Overall, our results indicate that L. salivarius CECT 30632 colonized, at least temporarily, the intestinal tract of the recruited elderly and may have contributed to improvements in their functional, nutritional, and immunological status, without changing the general structure of their nasal and fecal bacteriomes when assessed at the genus level. They also suggest the ability of low abundance bacteria to train immunity.

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.

In-process real-time probiotic phenotypic strain identity tracking: The use of Fourier transform infrared spectroscopy

Probiotic bacteria, capable of conferring benefits to the host, can present challenges in design, development, scale-up, manufacturing, commercialization, and life cycle management. Strain identification is one of the main quality parameters; nevertheless, this task can be challenging since established methodologies can lack resolution at the strain level for some microorganisms and\or are labor-intensive and time-consuming. Fourier transform infrared spectroscopy (FTIRS) has been largely used for the investigation of pathogenic species in the clinical field, whereas only recently has been proposed for the identification of probiotic strains. Within the probiotic industrial production, bacterial strains can be subjected to stressful conditions that may affect genomic and phenotypic characteristics; therefore, real-time monitoring of all the sequential growth steps is requested. Considering the fast, low-cost, and high-throughput features, FTIRS is an innovative and functional technology for typing probiotic strains from bench-top experiments to large-scale industrial production, allowing the monitoring of stability and identity of probiotic strains. In this study, the discriminatory power of FTIRS was assessed for four Lactiplantibacillus plantarum probiotic strains grown under different conditions, including temperatures (30 and 37°C) and medium (broth and agar), after consecutive sub-culturing steps. A comparison between the generated spectra with pulsed-field gel electrophoresis (PFGE) profiles was also performed. FTIRS was not only able to distinguish the strains of L. plantarum under different growth conditions but also to prove the phenotypic stability of L. plantarum type strain LP-CT after six growing steps. Regardless of the growth conditions, FTIRS spectra related to LP-CT constituted a unique hierarchical cluster, separated from the other L. plantarum strains. These results were confirmed by a PFGE analysis. In addition, based on FTIRS data, broth cultures demonstrated a higher reproducibility and discriminatory power with respect to agar ones. These results support the introduction of FTIRS in the probiotic industry, allowing for the step-by-step monitoring of massive microbial production while also guaranteeing the stability and purity of the probiotic strain. The proposed novel approach can constitute an impressive improvement in the probiotic manufacturing process.

Lactobacillus group and arterial hypertension: A broad review on effects and proposed mechanisms

Hypertension is the leading risk factor for cardiovascular diseases and is associated with intestinal dysbiosis with a decrease in beneficial microbiota. Probiotics can positively modulate the impaired microbiota and impart benefits to the cardiovascular system. Among them, the emended Lactobacillus has stood out as a microorganism capable of reducing blood pressure, being the target of several studies focused on managing hypertension. This review aimed to present the potential of Lactobacillus as an antihypertensive non-pharmacological strategy. We will address preclinical and clinical studies that support this proposal and the mechanisms of action by which these microorganisms reduce blood pressure or prevent its elevation.

Lactiplantibacillus plantarum LOC1 Isolated from Fresh Tea Leaves Modulates Macrophage Response to TLR4 Activation

Previously, we demonstrated that Lactiplantibacillus plantarum LOC1, originally isolated from fresh tea leaves, was able to improve epithelial barrier integrity in in vitro models, suggesting that this strain is an interesting probiotic candidate. In this work, we aimed to continue characterizing the potential probiotic properties of the LOC1 strain, focusing on its immunomodulatory properties in the context of innate immunity triggered by Toll-like receptor 4 (TLR4) activation. These studies were complemented by comparative and functional genomics analysis to characterize the bacterial genes involved in the immunomodulatory capacity. We carried out a transcriptomic study to evaluate the effect of L. plantarum LOC1 on the response of murine macrophages (RAW264.7 cells) to the activation of TLR4. We demonstrated that L. plantarum LOC1 exerts a modulatory effect on lipopolysaccharide (LPS)-induced inflammation, resulting in a differential regulation of immune factor expression in macrophages. The LOC1 strain markedly reduced the LPS-induced expression of some inflammatory cytokines (IL-1β, IL-12, and CSF2) and chemokines (CCL17, CCL28, CXCL3, CXCL13, CXCL1, and CX3CL1), while it significantly increased the expression of other cytokines (TNF-α, IL-6, IL-18, IFN-β, IFN-γ, and CSF3), chemokines (IL-15 and CXCL9), and activation markers (H2-k1, H2-M3, CD80, and CD86) in RAW macrophages. Our results show that L. plantarum LOC1 would enhance the intrinsic functions of macrophages, promoting their protective effects mediated by the stimulation of the Th1 response without affecting the regulatory mechanisms that help control inflammation. In addition, we sequenced the LOC1 genome and performed a genomic characterization. Genomic comparative analysis with the well-known immunomodulatory strains WCSF1 and CRL1506 demonstrated that L. plantarum LOC1 possess a set of adhesion factors and genes involved in the biosynthesis of teichoic acids and lipoproteins that could be involved in its immunomodulatory capacity. The results of this work can contribute to the development of immune-related functional foods containing L. plantarum LOC1.

Advances in characterization of probiotics and challenges in industrial application

An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.

Potential of New Bacterial Strains for a Multiproduct Bioprocess Application: A Case Study Using Isolates of Lactic Acid Bacteria from Pineapple Silage of Costa Rican Agro-Industrial Residues

Lactic acid bacteria (LAB) with potential for the development of multi-product processes are necessary for the valorization of side streams obtained during the biotechnological production of lactic acid (LA). In this study, 14 LAB strains isolated from pineapple agro-industrial residues in Costa Rica were cultivated in microplates, and the six strains with the highest growth were selected for fermentation in microbioreactors to evaluate the production of LA and acetic acid, and the consumption of glucose. Lacticaseibacillus paracasei 6710 and L. paracasei 6714 presented the highest OD600 values (1.600 and 1.602, respectively); however, the highest LA (in g/L) production was observed in L. paracasei 6714 (14.50 ± 0.20) and 6712 (14.67 ± 0.42). L. paracasei 6714 was selected for bioreactor fermentation and reached a maximum OD600 of 6.3062 ± 0.141, with a LA yield of 84.9% and a productivity of 1.06 g L−1 h−1 after 21 h of fermentation. Finally, lipoteichoic acid (LTA) detection from biomass was performed and the antimicrobial activity of the compounds present in the supernatant was studied. LTA was detected from L. paracasei 6714 biomass, and its supernatant caused significant inhibition of foodborne surrogate microorganisms. LAB isolated from pineapple silage have biotechnological potential for multiproduct processes.

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.

Probiotics and plant extracts: a promising synergy and delivery systems

There is a current interest in healthy diets and supplements, indicating the relevance of novel delivery systems for plant extracts rich in bioactive compounds and probiotics. This simultaneous delivery system can be prospective for health. In this sense, investigating foods rich in bioactive compounds or supplemented by them for incorporating probiotics and some approaches to improve probiotic survivability, such as the choice of resistant probiotic strains or microencapsulation, is valuable. This review addresses a brief discussion about the role of phenolic compounds, chlorophyll and carotenoids from plants and probiotics in gut health, indicating the benefits of this association. Also, an overview of delivery systems used in recent studies is shown, considering their advantages for incorporation in food matrices. Delivery systems containing compounds recovered from plants can reduce probiotic oxidative stress, improving survivability. However, investigating the beneficial concentration of some bioactive compounds from plant extracts is relevant due to their antimicrobial potential. In addition, further clinical trials and toxicological studies of plant extracts are pertinent to ensure safety. Thus, the recovery of extracts from plants emerges as an alternative to providing multiple compounds with antioxidant potential, increasing the preservation of probiotics and allowing the fortification or enrichment of food matrices.

Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening

IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.

Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov

The genera Convivina, Fructobacillus, Leuconostoc, Oenococcus and Weissella, which formed the family Leuconostocaceae, have recently been merged within the family Lactobacillaceae. Using genome sequences for 47 of the 52 named species from these genera, we report here comprehensive phylogenomic and comparative analyses on protein sequences from these species using multiple approaches. In a phylogenomic tree based on concatenated sequences of 498 core proteins from these five genera, and in a 16S rRNA gene tree, members of the genera Fructobacillus, Leuconostoc and Oenococcus formed distinct strongly supported clades. In contrast, Weissella species grouped into two distinct unrelated clades designated as the ‘Weissella main clade’ and ‘Weissella clade 2’. The presence of these clades is also seen in a matrix of pairwise average amino acid identity based on core protein sequences. In parallel, comparative genomic studies on protein sequences from Leuconostocaceae genomes have identified 46 conserved signature indels (CSIs) in diverse proteins that are unique characteristics of the different observed species clades. Of these identified CSIs, five, five and 13 CSIs are uniquely present in members of the genera Fructobacillus, Leuconostoc and Oenococcus, respectively. We also report here six and five CSIs that are exclusively present in the species from the Weissella main clade and Weissella clade 2, respectively, providing independent evidence supporting their distinctness from each other. The remaining 12 identified CSIs are commonly shared by some or all of the species from the genera Convivina, Fructobacillus and Leuconostoc, clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera Fructobacillus, Leuconostoc and Oenococcus as well as the two Weissella species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus Weissella be limited to only the species from the Weissella main clade, whereas the species forming Weissella clade 2 should be transferred to a new genus Periweissella gen. nov.

Genome Editing with Cas9 in Lactobacilli

The bacterial genus Lactobacillus comprises a vast range of strains with varying metabolic and probiotic traits, with genome editing representing an essential tool to probe genotype-phenotype relationships and enhance their beneficial properties. Currently, one of the most effective means of genome editing in bacteria couples low-efficiency recombineering with high-efficiency counterselection by nucleases from CRISPR-Cas systems. In lactobacilli, several CRISPR-based genome editing methods exist that have shown varying success in different strains. Here, we detail a fast and simple approach using two shuttle vectors encoding a recombineering template as well as the Streptococcus pyogenes Cas9, a trans-activating RNA, and a CRISPR array. We provide a step-by-step procedure for cloning the shuttle vectors, sequentially transforming the vectors into lactobacilli, screening for the desired edit, and finally clearing the shuttle vectors from the mutant strain. As CRISPR-based genome editing in bacteria can fail for various reasons, we also lay out instructions for probing mechanisms of escape. Finally, we include practical notes along the way to facilitate each stage of genome editing, and we illustrate the technique using a representative edit in a strain of Lactobacillus plantarum. Overall, this method should serve as a complete guide to performing genome editing in lactobacilli.

Common Inflammatory Mechanisms in COVID-19 and Parkinson's Diseases: The Role of Microbiome, Pharmabiotics and Postbiotics in Their Prevention

In the last decade, metagenomic studies have shown the key role of the gut microbiome in maintaining immune and neuroendocrine systems. Malfunction of the gut microbiome can induce inflammatory processes, oxidative stress, and cytokine storm. Dysfunction of the gut microbiome can be caused by short-term (virus infection and other infectious diseases) or long-term (environment, nutrition, and stress) factors. Here, we reviewed the inflammation and oxidative stress in neurodegenerative diseases and coronavirus infection (COVID-19). Here, we reviewed the renin-angiotensin-aldosterone system (RAAS) involved in the processes of formation of oxidative stress and inflammation in viral and neurodegenerative diseases. Moreover, the coronavirus uses ACE2 receptors of the RAAS to penetrate human cells. The coronavirus infection can be the trigger for neurodegenerative diseases by dysfunction of the RAAS. Pharmabiotics, postbiotics, and next-generation probiotics, are considered as a means to prevent oxidative stress, inflammatory processes, neurodegenerative and viral diseases through gut microbiome regulation.

The Dynamic Codon Biaser: calculating prokaryotic codon usage biases

Bacterial genomes often reflect a bias in the usage of codons. These biases are often most notable within highly expressed genes. While deviations in codon usage can be attributed to selection or mutational biases, they can also be functional, for example controlling gene expression or guiding protein structure. Several different metrics have been developed to identify biases in codon usage. Previously we released a database, CBDB: The Codon Bias Database, in which users could retrieve precalculated codon bias data for bacterial RefSeq genomes. With the increase of bacterial genome sequence data since its release a new tool was needed. Here we present the Dynamic Codon Biaser (DCB) tool, a web application that dynamically calculates the codon usage bias statistics of prokaryotic genomes. DCB bases these calculations on 40 different highly expressed genes (HEGs) that are highly conserved across different prokaryotic species. A user can either specify an NCBI accession number or upload their own sequence. DCB returns both the bias statistics and the genome’s HEG sequences. These calculations have several downstream applications, such as evolutionary studies and phage–host predictions. The source code is freely available, and the website is hosted at www.cbdb.info.

Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas

Genus Xanthomonas is a group of phytopathogens that is phylogenetically related to Xylella, Stenotrophomonas, and Pseudoxanthomonas, having diverse lifestyles. Xylella is a lethal plant pathogen with a highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas clades. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan-genome analysis identified a set of unique genes associated with sub-lineages representing plant-associated Xanthomonas clade and nosocomial origin Stenotrophomonas clade. Overall, our study reveals the importance of reconciling classical phenotypic data and genomic findings in reconstituting the taxonomic status of these four genera. SIGNIFICANCE STATEMENT: Xylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. An insect vector transmits the pathogen to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is significantly reduced both in terms of size (2 Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5 Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria and comparative studies, we assert the need to unify Xanthomonas with its relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor variant lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.

Health-Promoting Properties of Lacticaseibacillus paracasei: A Focus on Kefir Isolates and Exopolysaccharide-Producing Strains

Among artisanal fermented beverages, kefir (fermented milk drink) and water kefir (fermented nondairy beverage) are of special interest because their grains can be considered natural reservoirs of safe and potentially probiotic strains. In the last years, several reports on Lacticaseibacillus paracasei (formerly Lactobacillus paracasei) isolated from both artisanal fermented beverages were published focusing on their health-promoting properties. Although this is not the predominant species in kefir or water kefir, it may contribute to the health benefits associated to the consumption of the fermented beverage. Since the classification of L. paracasei has been a difficult task, the selection of an adequate method for identification, which is essential to avoid mislabeling in products, publications, and some publicly available DNA sequences, is discussed in the present work. The last findings in health promoting properties of L. paracasei and the bioactive compounds are described and compared to strains isolated from kefir, providing a special focus on exopolysaccharides as effector molecules. The knowledge of the state of the art of Lacticaseibacillus paracasei from kefir and water kefir can help to understand the contribution of these microorganisms to the health benefits of artisanal beverages as well as to discover new probiotic strains for applications in food industry.

Insights into 6S RNA in lactic acid bacteria (LAB)

BACKGROUND

6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB.

RESULTS

We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs.

CONCLUSIONS

Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.

Anticandidal Activities by Lactobacillus Species: An Update on Mechanisms of Action

Lactobacilli are among the most studied bacteria in the microbiome of the orodigestive and genitourinary tracts. As probiotics, lactobacilli may provide various benefits to the host. These benefits include regulating the composition of the resident microbiota, preventing - or even potentially reverting- a dysbiotic state. Candida albicans is an opportunistic pathogen that can influence and be influenced by other members of the mucosal microbiota and, under immune-compromising conditions, can cause disease. Lactobacillus and Candida species can colonize the same mucosal sites; however, certain Lactobacillus species display antifungal activities that can contribute to low Candida burdens and prevent fungal infection. Lactobacilli can produce metabolites with direct anticandidal function or enhance the host defense mechanisms against fungi. Most of the Lactobacillus spp. anticandidal mechanisms of action remain underexplored. This work aims to comprehensively review and provide an update on the current knowledge regarding these anticandidal mechanisms.

Replacement of Metaphylactic Antimicrobial Therapy by Oral Administration of Ligilactobacillus salivarius MP100 in a Pig Farm

Antibiotic use in swine production contributes to the emergence and spread of resistant bacteria, which poses a threat on human health. Therefore, alternative approaches must be developed. The objective of this work was the characterization of the probiotic properties of a Ligilactobacillus salivarius strain isolated from sow's milk and its application as an inoculated fermented feed to pregnant sows and piglets. The study was carried in a farm in which metaphylactic use of antimicrobials (including zinc oxide) was eliminated at the time of starting the probiotic intervention, which lasted for 2 years. Feces from 8-week-old piglets were collected before and after the treatment and microbiological and biochemical analyses were performed. The procedure led to an increase in the concentrations of clostridia and lactobacilli-related bacteria. Parallel, an increase in the concentration of butyrate, propionate and acetate was observed and a notable reduction in the presence of antibiotic resistant lactobacilli became apparent. In conclusion, replacement of antimicrobials by a microbiota-friendly approach was feasible and led to positive microbiological and biochemical changes in the enteric environment.

In Vivo Efficacy of Lacticaseibacillus rhamnosus L8020 in a Mouse Model of Oral Candidiasis

Oral candidiasis presents with multiple clinical manifestations. Among known pathogenic Candida species, Candida albicans is the most virulent and acts as the main causative fungus of oral candidiasis. Novel treatment modalities are needed because of emergent drug resistance and frequent candidiasis recurrence. Here, we evaluated the ability of Lacticaseibacillus rhamnosus L8020, isolated from healthy and caries-free volunteers, to prevent against the onset of oral candidiasis in a mouse model. Mice were infected with C. albicans, in the presence or absence of L. rhamnosus L8020. The mice were treated with antibiotics and corticosteroid to disrupt the oral microbiota and induce immunosuppression. We demonstrated that oral consumption of L. rhamnosus L8020 by C. albicans-infected mice abolished the pseudomembranous region of the mouse tongue; it also suppressed changes in the expression levels of pattern recognition receptor and chemokine genes. Our results suggest that L. rhamnosus L8020 has protective or therapeutic potential against oral candidiasis, which supports the potential use of this probiotic strain for oral health management.

Authenticity of probiotic foods and dietary supplements: A pivotal issue to address

The market of probiotic foods and supplements is growing rapidly but frequently the commercialized products are not compliant with their labels in terms of claimed probiotic strain(s) and labeled number of viable probiotic cells, thus mining the authenticity of these probiotic products.In this review, we provide an up-to-date overview of: (i) the current regulatory aspects, (ii) the consistency of probiotic foods and supplements with their labels, (iii) the implications of mislabeling on the quality, safety and functionality of these products and (iv) the available and most promising methods to assess the authenticity of these products, taking into account the need to discriminate among the different physiological states probiotics might be in the carrier matrices. It arises that authenticity of probiotic foods and supplements is an urgent issue, of industrial and legislation relevance, that need to be addressed. A plethora of methods are available to reach this goal, each with its own advantages and disadvantages. Protocols that combine the use of propidium monoazide (PMA) with metagenomics or polyphasic approaches including the PMA real time PCR or flow cytometry (for the viability assessment) and the whole genome sequence analysis (for the identification and typing of the probiotic strain) are the most promising that should be standardized and used by producers and regulators.

Functional Food for the Stimulation of the Immune System Against Malaria

Drug resistance has become a threat to global health, and new interventions are needed to control major infectious diseases. The composition of gut microbiota has been linked to human health and has been associated with severity of malaria. Fermented foods contribute to the community of healthy gut bacteria. Despite the studies connecting gut microbiota to the prevention of malaria transmission and severity, research on developing functional foods for the purpose of manipulating the gut microbiota for malaria control is limited. This review summarizes recent knowledge on the role of the gut microbiota in malaria prevention and treatment. This information should encourage the search for lactic acid bacteria expressing α-Gal and those that exhibit the desired immune stimulating properties for the development of functional food and probiotics for malaria control.

Unique niche-specific adaptation of fructophilic lactic acid bacteria and proposal of three Apilactobacillus species as novel members of the group

BACKGROUND

Fructophilic lactic acid bacteria (FLAB) found in D-fructose rich niches prefer D-fructose over D-glucose as a growth substrate. They need electron acceptors for growth on D-glucose. The organisms share carbohydrate metabolic properties. Fructobacillus spp., Apilactobacillus kunkeei, and Apilactobacillus apinorum are members of this unique group. Here we studied the fructophilic characteristics of recently described species Apilactobacillus micheneri, Apilactobacillus quenuiae, and Apilactobacillus timberlakei.

RESULTS

The three species prefer D-fructose over D-glucose and only metabolize D-glucose in the presence of electron acceptors. The genomic characteristics of the three species, i.e. small genomes and thus a low number of coding DNA sequences, few genes involved in carbohydrate transport and metabolism, and partial deletion of adhE gene, are characteristic of FLAB. The three species thus are novel members of FLAB. Reduction of genes involved in carbohydrate transport and metabolism in accordance with reduction of genome size were the common characteristics of the family Lactobacillaceae, but FLAB markedly reduced the gene numbers more than other species in the family. Pan-genome analysis of genes involved in metabolism displayed a lack of specific carbohydrate metabolic pathways in FLAB, leading to a unique cluster separation.

CONCLUSIONS

The present study expanded FLAB group. Fructose-rich environments have induced similar evolution in phylogenetically distant FLAB species. These are examples of convergent evolution of LAB.

Application of Ligilactobacillus salivarius CECT5713 to Achieve Term Pregnancies in Women with Repetitive Abortion or Infertility of Unknown Origin by Microbiological and Immunological Modulation of the Vaginal Ecosystem

In this study, the cervicovaginal environment of women with reproductive failure (repetitive abortion, infertility of unknown origin) was assessed and compared to that of healthy fertile women. Subsequently, the ability of Ligilactobacillus salivarius CECT5713 to increase pregnancy rates in women with reproductive failure was evaluated. Vaginal pH and Nugent score were higher in women with reproductive failure than in fertile women. The opposite was observed regarding the immune factors TGF-β 1, TFG-β 2, and VEFG. Lactobacilli were detected at a higher frequency and concentration in fertile women than in women with repetitive abortion or infertility. The metataxonomic study revealed that vaginal samples from fertile women were characterized by the high abundance of Lactobacillus sequences, while DNA from this genus was practically absent in one third of samples from women with reproductive failure. Daily oral administration of L. salivarius CECT5713 (~9 log₁₀ CFU/day) to women with reproductive failure for a maximum of 6 months resulted in an overall successful pregnancy rate of 56%. The probiotic intervention modified key microbiological, biochemical, and immunological parameters in women who got pregnant. In conclusion, L. salivarius CECT5713 has proved to be a good candidate to improve reproductive success in women with reproductive failure.

Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach

The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per μl DNA (equaling approximately 10 genome copies per μl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.

Combined transcriptomic and proteomic analysis of the response to bile stress in a centenarian-originated probiotic Lactobacillus salivarius Ren

Tolerance to bile stress is a crucial property for probiotics to survive in the gastrointestinal tract and exert their beneficial effects. In this work, transcriptomic analysis combined with two-dimensional electrophoresis revealed that the transcript levels of 129 genes and the abundance of 34 proteins were significantly changed in Lactobacillus salivarius Ren when exposed to 0.75 g/L ox-bile. Notably, carbohydrate metabolism shifted to the utilization of maltose and glycerol for energy production, suggesting that L. salivarius Ren expanded carbon sources profile for gut adaptation in response to bile. Moreover, the enzymes involved in cell surface charge modification and the cell envelope-located hemolysin-like protein were overproduced, which was supposed to hinder the penetration of bile. Then, the up-regulated ABC transporters could contribute to the extrusion of bile accumulated in the cytoplasm. Additionally, proteolytic system was activated to provide more amino acids for the synthesis and repair of proteins damaged by bile. Finally, γ-glutamylcysteine with antioxidant activity and oxidoreductases for redox homeostasis were increased to cope with the bile-induced oxidative stress. These findings provide new insights into the molecular mechanisms involved in bile stress response and adaptation in L. salivarius.

Reliability of MALDI-TOF mass spectrometry to identify oral isolates of Streptococcus salivarius and Lactobacillus spp

OBJECTIVE

The aim of this study is to evaluate the performance of MALDI-TOF mass spectrometry in identifying bacteria isolated in the oral cavity known to be of probiotic interest.

DESIGN

We evaluated Bruker MALDI Biotyper for the identification of 92 clinical oral isolates of probiotic interest (31 Streptococcus salivarius and 61 Lactobacillus spp.) by comparing direct colony method with on-plate formic acid extraction. Isolates were previously identified by use of biochemical methods and molecular biology.

RESULTS

Using the manufacturer's suggested genus and species level cutoff scores, the direct colony method identified 42 (45.7%) isolates at the genus level and 35 (38%) at the species level while the on-plate extraction method correctly identified 90 (97.8%) isolates at the genus level and 82 (89.1%) at the species level. The difference between the two methods was statistically significant at the genus and species levels (P ≤ 0.0001). After dividing the isolates into two subgroups, the analysis was repeated. The direct colony method identified correctly all isolates of Streptococcus salivarius at the species level. In contrast, the direct colony method allowed the identification of only 11 (18%) lactobacilli at the genus level and 4 (6.6%) at the species level. The on-plate extraction method was statistically (P ≤ 0.0001) more efficient since 59 (96.7%) lactobacilli were identified at the genus level and 51 (83.6%) at the species level.

CONCLUSIONS

MALDI Biotyper can efficiently identify Streptococcus salivarius regardless of the preparative method but on-plate extraction is superior to direct colony method for the identification of lactobacilli.

Strain-level epidemiology of microbial communities and the human microbiome

The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.

Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality

Lactobacillus species play a key role in the health of the urinary tract. For instance, Lactobacillus crispatus and L. jensenii have been found to inhibit uropathogenic Escherichia coli growth. While L. crispatus is typically found only within the microbiota of women without lower urinary tract symptoms (LUTS), L. jensenii has been found in the microbiota of women both with and without LUTS. With the recent introduction of the new species Lactobacillus mulieris, several strains of L. jensenii were reclassified as L. mulieris based upon gene marker and average nucleotide identity. We took a phylogenomic and comparative genomic approach to ascertain the genetic determinants of these two species. Looking at a larger data set, we identified additional L. mulieris strains, including one distinct from other members of the species—L. mulieris UMB7784. Furthermore, we identified unique loci in each species that may have clinical implications.

Lactobacilli are dominant members of the “healthy” female urogenital microbiota. One of these species, Lactobacillus jensenii, is routinely identified in the urinary microbiota of women both with and without urinary tract symptoms. In March 2020, the new bacterial species Lactobacillus mulieris was introduced, and phylogenetic and average nucleotide identity analysis identified eight L. jensenii strains that should be classified as members of the L. mulieris species. This prompted our phylogenomic study of all publicly available L. jensenii and L. mulieris genome sequences. While there is little variation in the 16S rRNA gene sequences, the core genome shows a clear distinction between genomes of the two species. We find eight additional strains of the species L. mulieris among these genomes. Furthermore, one strain, currently classified as L. mulieris UMB7784, is distinct from both L. jensenii and L. mulieris strains. As part of our comparative genomic study, we also investigated the genetic content that distinguishes these two species. Unique to the L. jensenii genomes are several genes related to catabolism of disaccharides. In contrast, L. mulieris genomes encode several cell surface and secreted proteins that are not found within the L. jensenii genomes. These L. jensenii-specific and L. mulieris-specific loci provide insight into phenotypic differences of these two species.

IMPORTANCELactobacillus species play a key role in the health of the urinary tract. For instance, Lactobacillus crispatus and L. jensenii have been found to inhibit uropathogenic Escherichia coli growth. While L. crispatus is typically found only within the microbiota of women without lower urinary tract symptoms (LUTS), L. jensenii has been found in the microbiota of women both with and without LUTS. With the recent introduction of the new species Lactobacillus mulieris, several strains of L. jensenii were reclassified as L. mulieris based upon gene marker and average nucleotide identity. We took a phylogenomic and comparative genomic approach to ascertain the genetic determinants of these two species. Looking at a larger data set, we identified additional L. mulieris strains, including one distinct from other members of the species—L. mulieris UMB7784. Furthermore, we identified unique loci in each species that may have clinical implications.

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.

Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, "Silenusvirus"

Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus "Silenusvirus".

Lactobacillus garii sp. nov., isolated from a fermented cassava product

A novel Gram-positive, catalase negative, rod-shaped strain, FI11369T, was isolated from gari, a traditional West African fermented food derived from cassava. Based on 16S rRNA gene sequence similarity, the closest type strains were Lactobacillus xiangfangensis LMG 26013T (99.4 % similarity), Lactobacillus plajomi NBRC 107333T (99.1 %), Lactobacillus paraplantarum DSM 10667T (99.1 %), Lactobacillus pentosus DSM 20314T (99.0 %), Lactobacillus plantarum subsp. plantarum ATCC 14917T (99.0 %), Lactobacillus modestisalitolerans NBRC 107235T (98.9 %), Lactobacillus plantarum subsp. argentoratensis DSM 16365T (98.9 %) and Lactobacillus daowaiensis NCIMB 15183T (98.8 %). The genome of strain FI11369T was sequenced and the average nucleotide identity (ANI) was compared with its closest relatives. ANI analysis showed that the closest relative, L. xiangfangensis DSM 27103T, had only a 82.4 % similarity. The main fatty acids of FI11369T were saturated C16 : 0 (18.2 %), unsaturated C18 : 1  ω9c (43.8 %) and cyclopropane C19 : 0 cyclo (ω10c and/or ω6; 22.5 %). Based on the genotypic and phenotypic data obtained in this study, a novel Lactobacillus species, Lactobacillus garii sp. nov., with the type strain FI11369T (=NCIMB 15148=DSM 108249), is proposed.

Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products

In societies that have food choices, conscious consumers demand natural solutions to keep their food healthy and fresh during storage, simultaneously reducing food waste. The use of “good bacteria” to protect food against spoilage organisms has a long, successful history, even though the molecular mechanisms are not fully understood. In this study, we show that the depletion of free manganese is a major bioprotective mechanism of lactobacilli in dairy products. High manganese uptake and intracellular storage provide a link to the distinct, nonenzymatic, manganese-catalyzed oxidative stress defense mechanism, previously described for certain lactobacilli. The evaluation of representative Lactobacillus species in our study identifies multiple relevant species groups for fungal growth inhibition via manganese depletion. Hence, through the natural mechanism of nutrient depletion, the use of dedicated bioprotective lactobacilli constitutes an attractive alternative to artificial preservation.

A prominent feature of lactic acid bacteria (LAB) is their ability to inhibit growth of spoilage organisms in food, but hitherto research efforts to establish the mechanisms underlying bioactivity focused on the production of antimicrobial compounds by LAB. We show, in this study, that competitive exclusion, i.e., competition for a limited resource by different organisms, is a major mechanism of fungal growth inhibition by lactobacilli in fermented dairy products. The depletion of the essential trace element manganese by two Lactobacillus species was uncovered as the main mechanism for growth inhibition of dairy spoilage yeast and molds. A manganese transporter (MntH1), representing one of the highest expressed gene products in both lactobacilli, facilitates the exhaustive manganese scavenging. Expression of the mntH1 gene was found to be strain dependent, affected by species coculturing and the growth phase. Further, deletion of the mntH1 gene in one of the strains resulted in a loss of bioactivity, proving this gene to be important for manganese depletion. The presence of an mntH gene displayed a distinct phylogenetic pattern within the Lactobacillus genus. Moreover, assaying the bioprotective ability in fermented milk of selected lactobacilli from 10 major phylogenetic groups identified a correlation between the presence of mntH and bioprotective activity. Thus, manganese scavenging emerges as a common trait within the Lactobacillus genus, but differences in expression result in some strains showing more bioprotective effect than others. In summary, competitive exclusion through ion depletion is herein reported as a novel mechanism in LAB to delay the growth of spoilage contaminants in dairy products.

IMPORTANCE In societies that have food choices, conscious consumers demand natural solutions to keep their food healthy and fresh during storage, simultaneously reducing food waste. The use of “good bacteria” to protect food against spoilage organisms has a long, successful history, even though the molecular mechanisms are not fully understood. In this study, we show that the depletion of free manganese is a major bioprotective mechanism of lactobacilli in dairy products. High manganese uptake and intracellular storage provide a link to the distinct, nonenzymatic, manganese-catalyzed oxidative stress defense mechanism, previously described for certain lactobacilli. The evaluation of representative Lactobacillus species in our study identifies multiple relevant species groups for fungal growth inhibition via manganese depletion. Hence, through the natural mechanism of nutrient depletion, the use of dedicated bioprotective lactobacilli constitutes an attractive alternative to artificial preservation.

Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group

One Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, and coccobacilli-shaped strain, designated c10Ua161MT, was isolated from a urine sample from a reproductive-age healthy woman. Comparative 16S rRNA gene sequence analysis indicated that strain c10Ua161MT belonged to the genus Lactobacillus . Phylogenetic analysis based on pheS and rpoA gene sequences strongly supported a clade encompassing strains c10Ua161MT and eight other strains from public databases, distinct from currently recognized species of the genus Lactobacillus. In silico Average Nucleotide Identity (ANI) and Genome-to-Genome Distance Calculator (GGDC), showed 87.9 and 34.3 % identity to the closest relative Lactobacillus jensenii , respectively. The major fatty acids of strain c10Ua161MT were C18 : 1ω9c (65.0%), C16 : 0 (17.8%), and summed feature 8 (10.2 %; comprising C18 : 1ω7c, and/or C18 : 1ω6c). The DNA G+C content of the strains is 34.2 mol%. On the basis of data presented here, strain c10Ua161MT represents a novel species of the genus Lactobacillus , for which the name Lactobacillus mulieris sp. nov. is proposed. The type strain is c10Ua161MT (=CECT 9755T=DSM 108704T).

Multi-Product Lactic Acid Bacteria Fermentations: A Review

Industrial biotechnology is a continuously expanding field focused on the application of microorganisms to produce chemicals using renewable sources as substrates. Currently, an increasing interest in new versatile processes, able to utilize a variety of substrates to obtain diverse products, can be observed. A robust microbial strain is critical in the creation of such processes. Lactic acid bacteria (LAB) are used to produce a wide variety of chemicals with high commercial interest. Lactic acid (LA) is the most predominant industrial product obtained from LAB fermentations, and its production is forecasted to rise as the result of the increasing demand of polylactic acid. Hence, the creation of new ways to revalorize LA production processes is of high interest and could further enhance its economic value. Therefore, this review explores some co-products of LA fermentations, derived from LAB, with special focus on bacteriocins, lipoteichoic acid, and probiotics. Finally, a multi-product process involving LA and the other compounds of interest is proposed.

Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA (2017-2019)

The qualified presumption of safety (QPS) was developed to provide a safety pre-assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as 'qualifications'. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS-recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019

Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

In recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.

Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea.

Adherence of Lactobacillus salivarius to HeLa Cells Promotes Changes in the Expression of the Genes Involved in Biosynthesis of Their Ligands

The attachment of a variety of Lactobacilli to the mucosal surfaces is accomplished through the interaction of OppA, a superficial bacterial protein also involved in oligopeptide internalization, and the glycosaminoglycan moiety of the proteoglycans that form the epithelial cell glycocalyx. Upon the interaction of the vaginal isolate Lactobacillus salivarius Lv72 and HeLa cell cultures, the expression of oppA increased more than 50-fold over the following 30 min, with the overexpression enduring, albeit at a lower rate, for up to 24 h. Conversely, transcriptional analysis of 62 genes involved in proteoglycan biosynthesis revealed generalized repression of genes whose products catalyze different steps of the whole pathway. This led to decreases in the superficial concentration of heparan (60%) and chondroitin sulfate (40%), although the molecular masses of these glycosaminoglycans were higher than those of the control cultures. Despite this lowering in the concentration of the receptor, attachment of the Lactobacilli proceeded, and completely overlaid the underlying HeLa cell culture.

Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position

Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex

The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on ∼2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences.

There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence.

IMPORTANCE The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on ∼2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences.

Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data

Identifying the microbes present in probiotic products is an important issue in product quality control and public health. The most common methods used to identify genera containing species that produce lactic acid are matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA sequence analysis. However, the high cost of operation, difficulty in distinguishing between similar species, and limitations of the current sequencing technologies have made it difficult to obtain accurate results using these tools. To overcome these problems, a whole-genome shotgun sequencing approach has been developed along with various metagenomic classification tools. Widely used tools include the marker gene and k-mer methods, but their inevitable false-positives (FPs) hampered an accurate analysis. We therefore, designed a coverage-based pipeline to reduce the FP problem and to achieve a more reliable identification of species. The coverage-based pipeline described here not only shows higher accuracy for the detection of species and proportion analysis, based on mapping depth, but can be applied regardless of the sequencing platform. We believe that the coverage-based pipeline described in this study can provide appropriate support for probiotic quality control, addressing current labeling issues.

Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group

The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402^T, had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.