Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features

Enhanced preservation of viability and species stratification in Lacticaseibacillus group using levan-fortified skim milk as a cryoprotectant during freeze-drying

Ensuring the viability and accurate stratification of Lacticaseibacillus group (LCG) species after freeze-drying is essential for their effective use as probiotics. This study investigates the use of reconstituted skim milk (RSM) as a cryoprotectant base, supplemented with fructans such as inulin and diverse forms of levan from Halomonas smyrnensis, to maintain the viability of Lacticaseibacillus casei ATCC 334, Lacticaseibacillus paracasei ATCC 25302, and Lacticaseibacillus rhamnosus ATCC 53103. Cellular viability was enhanced with levan-based cryoprotectants, motivating the use of levan-based hydrogels (gHLs) for freeze-drying LCG species. Throughout freeze-drying, the species-specific molecular masses (m/z) were preserved irrespective of the cryoprotectant used, with markers 3445 and 6664 m/z identified as potential species-specific molecular mass indicators for Lc. paracasei and Lc. rhamnosus, respectively. This study is the first to utilize levan in various forms as a cryoprotective agent alongside RSM, highlighting its promise as an effective cryoprotectant for LCG and potentially other probiotics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01802-x.

Whole genome sequencing of Lacticaseibacillus casei KACC92338 strain with strong antioxidant activity, reveals genes and gene clusters of probiotic and antimicrobial potential

Lacticaseibacillus casei KACC92338 was originally isolated from Korean raw milk. The antioxidant activities and protective effect in vitro of this strain were evaluated extensively. The results showed that KACC92338 can tolerate hydrogen peroxide up to 2 mM and cell-free supernatant (CFS) had higher scavenging rates for DPPH, hydroxyl radical, reducing power, and iron chelating activities with 95.61 ± 1.59%, 34.10 ± 1.93%, 2.220 ± 0.82 and 81.06 ± 1.06%, respectively. Meanwhile, the CFS showed a protective effect on yeast cells against 10 mM hydrogen peroxide with a survival rate of 76.05 ± 5.65%. To explore the probiotic potential of KACC92338, whole genome assembly and gene clusters with probiotic properties were further analyzed. The genome size was 3,050,901 bp with a 47.96% GC ratio, and 63 contigs. The genome contains 3,048 genes composed of 2,981 coding sequences and 67 RNAs (including 57 tRNAs +9 rRNAs +1 tmRNA). Average Nucleotide Identity and genome-based taxonomy showed that the KACC92338 genome had close similarity with L. casei strains with 96% ANI. Functional annotation by EggNOG and KEGG revealed the presence of numerous genes putatively involved in carbohydrate- and amino acid-transport and metabolism, genetic information processing, and signaling and cellular processes. Additionally, several genes conferring probiotic characteristics such as tolerance to stress, heat, cold, acid, bile salts, oxidative stress, immunomodulation, and adhesion to intestinal epithelium were identified. Notably absent were acquired antibiotic resistance genes, virulence, and pathogenic factors, that prove KACC92338 is a safe strain. Besides, the defense mechanisms of KACC92338 include six prophage regions and three clustered regularly interspaced short palindromic repeat (CRISPR) arrays as acquired immune systems against mobile elements. Further, the BAGEL4 database determined antimicrobial bacteriocin clusters of class IIb: sakacin-P, Enterolysin_A, sactipeptides, and Enterocin X, which suggests the strain could exhibit a wide range of antimicrobial functions. Together, these findings show that the L. casei KACC92338 strain can be a potential probiotic candidate in producing functional fermented foods-, health care- and skin care products- with antioxidant properties. However, a few more mechanistic studies are necessary on the safety assurance and potential application of the strain as a probiotic agent.

The Genome of Bifidobacterium longum subsp. infantis YLGB-1496 Provides Insights into Its Carbohydrate Utilization and Genetic Stability

Bifidobacterium longum subsp. infantis YLGB-1496 (YLGB-1496) is a probiotic strain isolated from human breast milk. The application of YLGB-1496 is influenced by carbohydrate utilization and genetic stability. This study used genome sequencing and morphology during continuous subculture to determine the carbohydrate utilization characteristics and genetic stability of YLGB-1496. The complete genome sequence of YLGB-1496 consists of 2,758,242 base pairs, 2442 coding sequences, and a GC content of 59.87%. A comparison of carbohydrate transport and metabolism genes of Bifidobacterium longum subsp. infantis (B. infantis) showed that YLGB-1496 was rich in glycosyl hydrolase 13, 20, 25, and 109 gene families. During continuous subculture, the growth characteristics and fermentation activity of the strain were highly stable. The bacterial cell surface and edges of the 1000th-generation strains were progressively smoother and well-defined, with no perforations or breaks in the cell wall. There were 20 SNP loci at the 1000th generation, fulfilling the requirement of belonging to the same strain. The presence of genes associated with cell adhesion and the absence of resistance genes supported the probiotic characteristics of the strain. The data obtained in this study provide insights into broad-spectrum carbohydrate utilization, genomic stability, and probiotic properties of YLGB-1496, which provide theoretical support to promote the use of YLGB-1496.

The quest for the perfect loaf of sourdough bread continues: Novel developments for selection of sourdough starter cultures

Sourdough fermentation, one of the oldest unit operations in food production, is currently experiencing a revival in bread production at the household, artisanal, and the industrial level. The expanding use of sourdough fermentation in bread production and the adaptation of fermentation to large scale industrial bread production also necessitate the development of novel starter cultures. Developments in the last years also have expanded the tools that are used to assess the metabolic potential of specific strains, species or genera of the Lactobacillaceae and have identified multiple ecological and metabolic traits as clade-specific. This review aims to provide an overview on the clade-specific metabolic potential of members of the Lactobacillaceae for use in sourdough baking, and the impact of these clade-specific traits on bread quality. Emphasis is placed on carbohydrate metabolism, including the conversion of sucrose and starch to soluble polysaccharides, conversion of amino acids, and the metabolism of organic acids. The current state of knowledge to compose multi-strain starter cultures (synthetic microbial communities) that are suitable for back-slopping will also be discussed. Taken together, the communication outlines the current tools for selection of microbes for use in sourdough baking.

Occurrence and genetic diversity of prophage sequences identified in the genomes of L. casei group bacteria

It is widely believed that microorganisms belonging to L. casei group can have positive effects on the human body. Therefore, these bacteria are used in many industrial processes, including the production of dietary supplements and probiotic preparations. When using live microorganisms in technological processes, it is important to use those without phage sequences within their genomes that can ultimately lead to lysis of the bacteria. It has been shown that many prophages have a benign nature, meaning that they don't directly lead to lysis or inhibit microbial growth. Moreover, the presence of phage sequences in the genomes of these bacteria increases their genetic diversity, which may contribute to easier colonization of new ecological niches. In the 439 analyzed genomes of the L. casei group, 1509 sequences of prophage origin were detected. The average length of intact prophage sequences analyzed was just under 36 kb. GC content of tested sequences was similar for all analyzed species (44.6 ± 0.9%). Analyzing the protein coding sequences collectively, it was found that there was an average of 44 putative ORFs per genome, while the ORF density of all phage genomes varied from 0.5 to 2.1. The average nucleotide identity calculated on sequence alignments for analyzed sequences was 32.7%. Of the 56 L. casei strains used in the next part of the study, 32 did not show culture growth above the OD600 value of 0.5, even at a mitomycin C concentration of 0.25 μg/ml. Primers used for this study allowed for the detection of prophage sequences for over 90% of tested bacterial strains. Finally, prophages of selected strains were induced using mitomycin C, phage particles were isolated and then genomes of viruses obtained were sequenced and analyzed.

Bartonella Prevalence and Genome Sequences in Rodents in Some Regions of Xinjiang, China

In this study, we investigated Bartonella infection and its genetic diversity in rodents in Beitun, Xinjiang Uygur Autonomous Region, China. Small mammals were captured using snap traps at four sampling sites in 2018. Spleen and liver tissues were collected and cultured to isolate Bartonella strains. Whole-genome sequencing was performed on the strains identified as Bartonella by gltA gene PCR, and the average nucleotide identity (ANI) of the genomes was calculated by using FastANI v1.33. Phylogenetic trees were constructed for the samples positive for Bartonella spp. by the gltA PCR assay based on 1,290-bp gltA genes, 2,903-bp rpoB genes, and core-genome single nucleotide polymorphisms (SNPs). Among 66 rodents, 11 were positive for Bartonella, with an infection rate of 16.67%. The rodent infection rates in different tissues (χ2 = 2.133; P = 0.242), species (χ2 = 9.631; P = 0.141), and habitats (χ2 = 4.309; P = 0.312) did not show statistical differences. Bartonella spp. isolated from the rodents were phylogenetically divided into six clades (two different Bartonella species were detected in two rodents). By comparing phylogenetic trees based on gltA genes, rpoB genes, and SNPs, we found that the topological structures of several evolutionary trees are different. However, the Bartonella strains isolated in this study were clustered into six clusters in different phylogenetic trees. Broad distributions and high genetic diversity of Bartonella strains were observed among rodents in Beitun, Xinjiang. IMPORTANCE Rodent-borne Bartonella species have been associated with zoonotic diseases. Bartonella species such as Bartonella elizabethae, Bartonella grahamii, and Bartonella tribocorum can cause disease in humans. Humans can be infected by blood-sucking arthropods through the scratches and bites of an infected reservoir host or via contact with infectious rodents. Xinjiang is one of the provinces with the most abundant species of Bartonella in China, but there are few reports about the prevalence of Bartonella in the Beitun area. This research aims to investigate the occurrence and prevalence of Bartonella infection in rodents at these sampling sites and provide a basis for the prevention and control of rodent Bartonella species in Beitun and the surrounding areas of Xinjiang.

Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments

Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.

Queijo Serra da Estrela PDO Cheese: Investigation into Its Morpho-Textural Traits, Microbiota, and Volatilome

Queijo Serra da Estrela is a PDO Portuguese cheese produced through coagulation of raw ewe’s milk using cardoon (Cynara cardunculus L.) flowers. The present research was aimed at depicting an up-to-date and comprehensive overview of the microbiota of Queijo Serra da Estrela cheese. To this end, viable counting and metataxonomic analysis were carried out on cheeses sampled from four Portuguese artisan producers. Physico-chemical and morpho-textural analyses were also performed, together with the analysis of volatile organic compounds (VOCs). Finally, non-starter lactic acid bacteria (NSLAB) isolated from the cheeses were characterized for their enzymatic activities using a semi-quantitative method. According to the metataxonomic analysis, Lactococcus lactis and Lactococcus piscium were the species occurring at the highest relative abundance. The isolates collected from the cheeses were assigned to Enterococcus durans, Enterococcus faecalis, Enterococcus faecium, Enterococcus lactis, Levilactobacillus brevis, Latilactobacillus graminis, Leuconostoc mesenteroides, and the Lacticaseibacillus casei group. The enzymatic characterization of these cultures highlighted esterase, aminopeptidase, acid phosphatase, beta-galactosidase, alpha-glucosidase, and beta-glucosidase among the major enzymatic activities. Fungal populations were dominated by Debaryomyces hansenii and Kurtzmaniella zeylanoides; however, species rarely found in cheese (e.g., Candida boidinii, Vishniacozyma victoriae, and Starmerella) were also detected. The volatile compounds characterizing the analyzed cheeses were carboxylic acids and esters, followed by carbonyl compounds and alcohols.

New perspectives on an old grouping: The genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention

Oxalobacter formigenes is a unique bacterium with the ability to metabolize oxalate as a primary carbon source. Most kidney stones in humans are composed of calcium and oxalate. Therefore, supplementation with an oxalate-degrading bacterium may reduce stone burden in patients suffering from recurrent calcium oxalate-based urolithiasis. Strains of O. formigenes are divided into two groups: group I and group II. However, the differences between strains from each group remain unclear and elucidating these distinctions will provide a better understanding of their physiology and potential clinical applications. Here, genomes from multiple O. formigenes strains underwent whole genome sequencing followed by phylogenetic and functional analyses. Genetic differences suggest that the O. formigenes taxon should be divided into an additional three species: Oxalobacter aliiformigenes sp. nov, Oxalobacter paeniformigenes sp. nov, and Oxalobacter paraformigenes sp. nov. Despite the similarities in the oxalyl-CoA gene (oxc), which is essential for oxalate degradation, these strains have multiple unique genetic features that may be potential exploited for clinical use. Further investigation into the growth of these strains in a simulated fecal environment revealed that O. aliiformigenes strains are capable of thriving within the human gut microbiota. O. aliiformigenes may be a better therapeutic candidate than current group I strains (retaining the name O. formigenes), which have been previously tested and shown to be ineffective as an oral supplement to mitigate stone disease. By performing genomic analyses and identifying these novel characteristics, Oxalobacter strains better suited to mitigation of calcium oxalate-based urolithiasis may be identified in the future.

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections

Respiratory viruses such as influenza viruses, respiratory syncytial virus (RSV), and coronaviruses initiate infection at the mucosal surfaces of the upper respiratory tract (URT), where the resident respiratory microbiome has an important gatekeeper function. In contrast to gut-targeting administration of beneficial bacteria against respiratory viral disease, topical URT administration of probiotics is currently underexplored, especially for the prevention and/or treatment of viral infections. Here, we report the formulation of a throat spray with live lactobacilli exhibiting several in vitro mechanisms of action against respiratory viral infections, including induction of interferon regulatory pathways and direct inhibition of respiratory viruses. Rational selection of Lactobacillaceae strains was based on previously documented beneficial properties, up-scaling and industrial production characteristics, clinical safety parameters, and potential antiviral and immunostimulatory efficacy in the URT demonstrated in this study. Using a three-step selection strategy, three strains were selected and further tested in vitro antiviral assays and in formulations: Lacticaseibacillus casei AMBR2 as a promising endogenous candidate URT probiotic with previously reported barrier-enhancing and anti-pathogenic properties and the two well-studied model strains Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1 that display immunomodulatory capacities. The three strains and their combination significantly reduced the cytopathogenic effects of RSV, influenza A/H1N1 and B viruses, and HCoV-229E coronavirus in co-culture models with bacteria, virus, and host cells. Subsequently, these strains were formulated in a throat spray and human monocytes were employed to confirm the formulation process did not reduce the interferon regulatory pathway-inducing capacity. Administration of the throat spray in healthy volunteers revealed that the lactobacilli were capable of temporary colonization of the throat in a metabolically active form. Thus, the developed spray with live lactobacilli will be further explored in the clinic as a potential broad-acting live biotherapeutic strategy against respiratory viral diseases.

After the storm-Perspectives on the taxonomy of Lactobacillaceae

In 2020, a taxonomic reorganization of the lactic acid bacteria reclassified over 300 species in 7 genera and 2 families into one family, the Lactobacillaceae, with 31 genera including 23 new genera to include organisms formerly classified as Lactobacillus species. This communication aims to provide a debrief on the taxonomic reorganization of lactobacilli to identify shortcomings in the proposed taxonomic framework, and to outline perspectives and opportunities provided by the current taxonomy of the Lactobacillaceae. The current taxonomy of lactobacilli not only necessitates becoming familiar with 23 new genus names but also provides substantial new opportunities in scientific discovery and regulatory approval of these organisms. First, description of new species in the Lactobacillaceae is facilitated and a solid framework for description of novel genera is provided. Second, the current taxonomy greatly enhances the resolution of genus-level sequencing approaches (e.g., 16S rRNA-based metagenomics) when identifying the composition and function of microbial communities. Third, the current taxonomy greatly facilitates the formulation of hypotheses linking phylogeny to metabolism and ecology of lactobacilli.

Comprehensive Analysis of the Nocardia cyriacigeorgica Complex Reveals Five Species-Level Clades with Different Evolutionary and Pathogenicity Characteristics

Nocardia cyriacigeorgica is a common etiological agent of nocardiosis that has increasingly been implicated in serious pulmonary infections, especially in immunocompromised individuals. However, the evolution, diversity, and pathogenesis of N. cyriacigeorgica have remained unclear. Here, we performed a comparative genomic analysis using 91 N. cyriacigeorgica strains, 45 of which were newly sequenced in this study. Phylogenetic and average nucleotide identity (ANI) analyses revealed that N. cyriacigeorgica contained five species-level clades (8.6 to 14.6% interclade genetic divergence), namely, the N. cyriacigeorgica complex (NCC). Further pan-genome analysis revealed extensive differences among the five clades in nine functional categories, such as energy production, lipid metabolism, secondary metabolites, and signal transduction mechanisms. All 2,935 single-copy core genes undergoing purifying selection were highly conserved across NCC. However, clades D and E exhibited reduced selective constraints, compared to clades A to C. Horizontal gene transfer (HGT) and mobile genetic elements contributed to genomic plasticity, and clades A and B had experienced a higher level of HGT events than other clades. A total of 129 virulence factors were ubiquitous across NCC, such as the mce operon, hemolysin, and type VII secretion system (T7SS). However, different distributions of three toxin-coding genes and two new types of mce operons were detected, which might contribute to pathogenicity differences among the members of the NCC. Overall, our study provides comprehensive insights into the evolution, genetic diversity, and pathogenicity of NCC, facilitating the prevention of infections.

IMPORTANCENocardia species are opportunistic bacterial pathogens that can affect all organ systems, primarily the skin, lungs, and brain. N. cyriacigeorgica is the most prevalent species within the genus, exhibits clinical significance, and can cause severe infections when disseminated throughout the body. However, the evolution, diversity, and pathogenicity of N. cyriacigeorgica remain unclear. Here, we have conducted a comparative genomic analysis of 91 N. cyriacigeorgica strains and revealed that N. cyriacigeorgica is not a single species but is composed of five closely related species. In addition, we discovered that these five species differ in many ways, involving selection pressure, horizontal gene transfer, functional capacity, pathogenicity, and antibiotic resistance. Overall, our work provides important clues in dissecting the evolution, genetic diversity, and pathogenicity of NCC, thereby advancing prevention measures against these infections.

Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Thirteen Gram-positive, catalase-positive, rod-shaped single colonies were obtained after culturing a strawberry leaf on de Man–Rogosa–Sharpe agar. Based on 16S rRNA gene and rpoA gene sequence similarities, ranging between 99.0–100% and 96.5–100%, respectively, the 13 isolates were found to be closely related to each other. Two of the independent isolates, AMBP162^T and AMBP252, were whole-genome sequenced, and showed to be undistinguishable with an average nucleotide identity (ANI) value of 100 %. Compared to the reference genomes for all species in the family Lactobacillaceae, the AMBP162^T genome was most similar to the reference strain of Latilactobacillus curvatus with ANI of only 89.5 %, indicating they were a different species. Based on genotypic and phenotypic data, a novel Latilactobacillus species, Latilactobacillus fragifolii sp. nov., with the type strain AMBP162^T (=LMG 32285^T=CECT 30357^T) is proposed.

Inhibition of Bacterial Adhesion and Antibiofilm Activities of a Glycolipid Biosurfactant from Lactobacillus rhamnosus with Its Physicochemical and Functional Properties

Biosurfactants derived from different microbes are an alternative to chemical surfactants, which have broad applications in food, oil, biodegradation, cosmetic, agriculture, pesticide and medicine/pharmaceutical industries. This is due to their environmentally friendly, biocompatible, biodegradable, effectiveness to work under various environmental conditions and non-toxic nature. Lactic acid bacteria (LAB)-derived glycolipid biosurfactants can play a major role in preventing bacterial attachment, biofilm eradication and related infections in various clinical settings and industries. Hence, it is important to explore and identify the novel molecule/method for the treatment of biofilms of pathogenic bacteria. In the present study, a probiotic Lactobacillus rhamnosus (L. rhamnosus) strain was isolated from human breast milk. Firstly, its ability to produce biosurfactants, and its physicochemical and functional properties (critical micelle concentration (CMC), reduction in surface tension, emulsification index (% EI24), etc.) were evaluated. Secondly, inhibition of bacterial adhesion and biofilm eradication by cell-bound biosurfactants from L. rhamnosus was performed against various biofilm-forming pathogens (B. subtilis, P. aeruginosa, S. aureus and E. coli). Finally, bacterial cell damage, viability of cells within the biofilm, exopolysaccharide (EPS) production and identification of the structural analogues of the crude biosurfactant via gas chromatography-mass spectrometry (GC-MS) analysis were also evaluated. As a result, L. rhamnosus was found to produce 4.32 ± 0.19 g/L biosurfactant that displayed a CMC of 3.0 g/L and reduced the surface tension from 71.12 ± 0.73 mN/m to 41.76 ± 0.60 mN/m. L. rhamnosus cell-bound crude biosurfactant was found to be effective against all the tested bacterial pathogens. It displayed potent anti-adhesion and antibiofilm ability by inhibiting the bacterial attachment to surfaces, leading to the disruption of biofilm formation by altering the integrity and viability of bacterial cells within biofilms. Our results also confirm the ability of the L. rhamnosus cell-bound-derived biosurfactant to damage the architecture of the biofilm matrix, as a result of the reduced total EPS content. Our findings may be further explored as a green alternative/approach to chemically synthesized toxic antibiofilm agents for controlling bacterial adhesion and biofilm eradication.

Real-Time PCR Method for the Rapid Detection and Quantification of Pathogenic Staphylococcus Species Based on Novel Molecular Target Genes

Coagulase-positive Staphylococcus aureus is a foodborne pathogen considered one of the causes of food-related disease outbreaks. Like S. aureus, Staphylococcus capitis, Staphylococcus caprae, and S. epidermidis are opportunistic pathogens causing clinical infections and food contamination. The objective of our study was to develop a rapid, accurate, and monitoring technique to detect four Staphylococcus species in food. Four novel molecular targets (GntR family transcriptional regulator for S. aureus, phosphomannomutase for S. epidermidis, FAD-dependent urate hydroxylase for S. capitis, and Gram-positive signal peptide protein for S. caprae) were mined based on pan-genome analysis. Primers targeting molecular target genes showed 100% specificity for 100 non-target reference strains. The detection limit in pure cultures and artificially contaminated food samples was 10² colony-forming unit/mL for S. aureus, S. capitis, S. caprae, and S. epidermidis. Moreover, real-time polymerase chain reaction successfully detected strains isolated from various food matrices. Thus, our method allows an accurate and rapid monitoring of Staphylococcus species and may help control staphylococcal contamination of food.

In vitro Inhibition of respiratory pathogens by lactobacillus and alpha haemolytic streptococci from Aboriginal and Torres Strait Islander children

AIMS

To explore the in vitro ability of alpha haemolytic streptococcus (AHS) and lactobacilli (LBs), from Indigenous Australian children, to inhibit the growth of respiratory pathogens (Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis), also from Indigenous Australian children.

METHODS AND RESULTS

The bacterial interference of 91 isolates, from Indigenous Australian children both with and without otitis media (OM) or rhinorrhoea, was investigated using agar overlay and cell-free supernatant. Promising isolates underwent whole genome sequencing to investigate upper respiratory tract tropism, antibiotic resistance and virulence. Antibiotic susceptibility was examined for ampicillin, amoxicillin +clavulanic acid and azithromycin. Differences in the strength of bacterial inferences in relation to OM was examined using a case series of three healthy and three children with OM. LBs readily inhibited the growth of pathogens. AHS were less effective, although several isolates inhibited S. pneumoniae. One L. rhamnosus had genes coding for pili to adhere to epithelial cells. We detected antibiotic resistance genes coding for antibiotic efflux pump and ribosomal protection protein. LBs were susceptible to antimicrobials in vitro. Screening for virulence detected genes encoding for two putative capsule proteins. Healthy children had AHS and LB that were more potent inhibitors of respiratory pathogens in vitro than children with OM.

CONCLUSIONS

L. rhamnosus from remote Indigenous Australian children are potent inhibitors of respiratory pathogens in vitro.

SIGNIFICANCE AND IMPACT OF STUDY

Respiratory/ear disease are endemic in Indigenous Australians. There is an urgent call for more effective treatment/prevention; beneficial microbes have not been explored. L. rhamnosus investigated in this study are potent inhibitors of respiratory pathogens in vitro and require further investigation.

The nasal mutualist Dolosigranulum pigrum AMBR11 supports homeostasis via multiple mechanisms

Comparing the nasal microbiome of healthy individuals and chronic rhinosinusitis (CRS) patients revealed Dolosigranulum pigrum as a species clearly associated with nasal health, although isolates obtained from healthy individuals are scarce. In this study, we explored the properties of this understudied lactic acid bacterium by integrating comparative genomics, habitat mining, cultivation, and functional characterization of interaction capacities. Mining 10.000 samples from the Earth Microbiome Project of 17 habitat types revealed that Dolosigranulum is mainly associated with the human nasal cavity. D. pigrum AMBR11 isolated from the nose of a healthy individual exerted antimicrobial activity against Staphylococcus aureus, decreased proinflammatory cytokine production in airway epithelial cells, and Galleria mellonella larvae mortality induced by this important nasal pathobiont. Furthermore, the strain protected the nasal barrier function in a mouse model using interleukin-4 as disruptive cytokine. Hence, D. pigrum AMBR11 is a mutualist with high potential as topical live biotherapeutic product.

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.

Differentiation of Lacticaseibacillus zeae Using Pan-Genome Analysis and Real-Time PCR Method Targeting a Unique Gene

Lacticaseibacillus zeae strains, isolated from raw milk and fermented dairy products, are closely related to the Lacticaseibacillus species that has beneficial probiotic properties. However, it is difficult to distinguish those using conventional methods. In this study, a unique gene was revealed to differentiate L. zeae from other strains of the Lacticaseibacillus species and other species by pan-genome analysis, and a real-time PCR method was developed to rapidly and accurately detect the unique gene. The genome analysis of 141 genomes yielded an 17,978 pan-genome. Among them, 18 accessory genes were specifically present in five genomes of L. zeae. The glycosyltransferase family 8 was identified as a unique gene present only in L. zeae and not in 136 other genomes. A primer designed from the unique gene accurately distinguished L. zeae in pure and mixed DNA and successfully constructed the criterion for the quantified standard curve in real-time PCR. The real-time PCR method was applied to 61 strains containing other Lacticaseibacillus species and distinguished L. zeae with 100% accuracy. Also, the real-time PCR method was proven to be superior to the 16S rRNA gene method in the identification of L. zeae.

Genomic analysis revealed conserved acid tolerance mechanisms from native micro-organisms in fermented feed

AIMS

Fermented feed is an agricultural practice used in many regions of the world to improve the growth performance of farm animals. This study aimed to identify and evaluate the lactic acid bacteria and yeast involved in the production of fermented feed.

METHODS AND RESULTS

We isolated and described two micro-organisms from autochthonous microbiota origin present in a regional feed product, Lactobacillus paracasei IBR07 (Lacticaseibacillus paracasei) and Kazachstania unispora IBR014 (Saccharomyces unisporum). Genome sequence analyses were performed to characterize both micro-organisms. Potential pathways involved in the acid response, tolerance and persistence were predicted in both genomes. Although L. paracasei and K. unispora are considered safe for animal feed, we analysed the presence of virulence factors, antibiotic resistance and pathogenicity islands. Furthermore, the Galleria mellonella model was used to support the safety of both isolates.

CONCLUSIONS

We conclude that IBR07 and IBR014 strains are good candidates to be used as starter cultures for feed fermentation.

SIGNIFICANCE AND IMPACT OF THE STUDY

The data presented here will be helpful to explore other biotechnological aspects and constitute a starting point for further studies to establish the consumption benefit of fermented feed in farm animal production.

Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model

BACKGROUND

Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear.

RESULTS

By population genomic analysis of 418 Bifidobacterium longum strains, including 143 newly sequenced in this study, three geographically distinct gene pools/populations, BLAsia1, BLAsia2, and BLothers, were identified. Genes involved in cell wall biosynthesis, particularly peptidoglycan biosynthesis, varied considerably among the core genomes of the different populations, but accessory genes that contributed to the carbohydrate metabolism were significantly distinct. Although active transmission was observed inter-host, inter-country, inter-city, intra-community, and intra-family, a single B. longum clone seemed to reside within each individual. A significant negative association was observed between host age and relative abundance of B. longum, while there was a strong positive association between host age and strain genotype [e.g., single nucleotide polymorphisms in the arginine biosynthesis pathway]. Further animal experiments performed with the B. longum isolates via using a D-galactose-induced aging mouse model supported these associations, in which B. longum strains with different genotypes in arginine biosynthesis pathway showed divergent abilities on protecting against host aging possibly via their different abilities to modify the metabolism of gut microbes.

CONCLUSIONS

This is the first known example of research on the evolutionary history and transmission of this probiotic species. Our results propose a new mechanistic insight for promoting host longevity via the informed use of specific probiotics or molecules. Video abstract.

Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

Nocardia species can be responsible for opportunistic infections in humans, causing a variety of clinical presentations. They can also cause mycetoma in a normal host through direct inoculation. Although these species are often overlooked and misunderstood by modern medicine, they can cause life-threatening infections. However, most of our knowledge about Nocardia is based upon case reports and a few small studies of limited scope. This study provides an overview of the taxonomic and evolutionary structure of the genus Nocardia through extensive analysis of genome sequences. Our work aids the field by dissecting the genetic diversity of this species and improving the identification scheme for Nocardia species.

Manganese accumulation in probiotic Lactobacillus paracasei ATCC 55544 analyzed by synchrotron X-ray fluorescence microscopy and impact of accumulation on the bacterial viability following encapsulation

Lactobacillus spp. are known to accumulate large amounts of inorganic manganese, which protects against oxidative damage by scavenging free radicals. The ability of probiotic L. paracasei ATCC 55544 to maintain viability during long-term ambient storage may be enhanced by this microorganism's ability to accumulate manganese, which may act as a free radical scavenger. To investigate this hypothesis, X-ray fluorescence microscopy (XFM) was employed to determine the changes in the elemental composition of L. paracasei during growth in the MRS medium with or without added manganese. Moreover, manganese uptake by cells as a function of physiological growth state, early log vs. stationary phase was evaluated. The semiquantitative X-ray fluorescence microscopy results revealed that lower levels of manganese accumulation occurred during the early log phase of bacterial growth of L. paracasei cells (0.0064 µg/cm²) compared with the stationary phase cells (0.1355 µg/cm²). L. paracasei cells grown in manganese deficient MRS medium resulted in lower manganese uptake by cells (0.0027 µg/cm²). The L. paracasei cells were further embedded in milk powder matrix using a fluidized-bed drying technique and stored at a water activity (a_w) of 0.33 at 25 °C for 15 days. The viability counts of L. paracasei cells grown in MRS medium harvested after 18 h growth and embedded in milk powder matrix retained viability of (9.19 ± 0.12 log CFU/g). No viable L. paracasei cells were observed in the case of embedded L. paracasei cells grown in manganese-deficient MRS medium harvested after 18 h growth or in the case of L. paracasei cells harvested after 4 h when grown in MRS medium. The lower level of manganese accumulation was found to be related to the loss of bacterial viability during storage.

Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens

Lactobacillus crispatus is the dominant species in the vagina of many women. With the potential for strains of this species to be used as a probiotic to help prevent and treat dysbiosis, we investigated isolates from vaginal swabs with Lactobacillus-dominated and a dysbiotic microbiota. A comparative genome analysis led to the identification of metabolic pathways for synthesis and degradation of three major biogenic amines in most strains. However, targeted metabolomic analysis of the production and degradation of biogenic amines showed that certain strains have either the ability to produce or to degrade these compounds. Notably, six strains produced cadaverine, one produced putrescine, and two produced tyramine. These biogenic amines are known to raise vaginal pH, cause malodour, and make the environment more favourable to vaginal pathogens. In vitro experiments confirmed that strains isolated from women with a dysbiotic vaginal microbiota have higher antimicrobial effects against the common urogenital pathogens Escherichia coli and Enterococcus faecium. The results indicate that not all L. crispatus vaginal strains appear suitable for probiotic application and the basis for selection should not be only the overall composition of the vaginal microbiota of the host from which they came, but specific biochemical and genetic traits.

Real-time PCR method for qualitative and quantitative detection of Lactobacillus sakei group species targeting novel markers based on bioinformatics analysis

Latilactobacillus sakei group comprises four closely related species, making it difficult to accurately distinguish them with standard markers such as the 16S rRNA gene. The objective of our study was to mine novel markers for PCR detection and discrimination of L. sakei group species and L. sakei subspecies by comparative pan-genomic analysis. A total of 63 genome sequences of L. sakei group species consisted of 119,899 coding genes, yielding 5741 pan-genomes, 831 core-genomes, 3347 accessory-genomes, and 1563 unique-genomes. The accessory-genome was compared to extract unique candidate genes common only to genomes of the same species. The candidate genes were then aligned with the other bacterial genomes to select marker genes present in all genomes of a given species, but not in the genomes of other species. We identified the arginine/ornithine antiporter, putative cell surface protein precursor, sodium:solute symporter, PRD domain protein, PTS sugar transporter subunit IIC, and phosphoenolpyruvate-dependent sugar phosphotransferase system EIIC as marker genes for L. sakei, L. sakei subsp. sakei, L. sakei subsp. carnosus, L. curvatus, L. graminis, and L. fuchuensis, respectively. Primer pairs were designed for each marker and showed 100% specificity for 48 lactic acid bacterial reference strains. The PCR method developed in this study was used to evaluate 106 strains isolated from fermented foods to demonstrate that the marker genes provided a viable alternative to the 16S rRNA gene. We also applied the method to the monitoring of kimchi samples to quantify L. sakei group species or subspecies. Our PCR method based on novel markers can rapidly identify L. sakei group with high accuracy and high throughput.

Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species

Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.

Quantitative Detection of Bifidobacterium longum Strains in Feces Using Strain-Specific Primers

We adopted a bioinformatics-based technique to identify strain-specific markers, which were then used to quantify the abundances of three distinct B. longum sup. longum strains in fecal samples of humans and mice. A pangenome analysis of 205 B. longum sup. longum genomes revealed the accumulation of considerable strain-specific genes within this species; specifically, 28.7% of the total identified genes were strain-specific. We identified 32, 14, and 49 genes specific to B. longum sup. longum RG4-1, B. longum sup. longum M1-20-R01-3, and B. longum sup. longum FGSZY6M4, respectively. After performing an in silico validation of these strain-specific markers using a nucleotide BLAST against both the B. longum sup. longum genome database and an NR/NT database, RG4-1_01874 (1331 bp), M1-20-R01-3_00324 (1745 bp), and FGSZY6M4_01477 (1691 bp) were chosen as target genes for strain-specific quantification. The specificities of the qPCR primers were validated against 47 non-target microorganisms and fecal baseline microbiota to ensure that they produced no PCR amplification products. The performance of the qPCR primer-based analysis was further assessed using fecal samples. After oral administration, the target B. longum strains appeared to efficiently colonize both the human and mouse guts, with average population levels of >108 CFU/g feces. The bioinformatics pipeline proposed here can be applied to the quantification of various bacterial species.

Lactobacilli Have a Niche in the Human Nose

Although an increasing number of beneficial microbiome members are characterized for the human gut and vagina, beneficial microbes are underexplored for the human upper respiratory tract (URT). In this study, we demonstrate that taxa from the beneficial Lactobacillus genus complex are more prevalent in the healthy URT than in patients with chronic rhinosinusitis (CRS). Several URT-specific isolates are cultured, characterized, and further explored for their genetic and functional properties related to adaptation to the URT. Catalase genes are found in the identified lactobacilli, which is a unique feature within this mostly facultative anaerobic genus. Moreover, one of our isolated strains, Lactobacillus casei AMBR2, contains fimbriae that enable strong adherence to URT epithelium, inhibit the growth and virulence of several URT pathogens, and successfully colonize nasal epithelium of healthy volunteers. This study thus demonstrates that specific lactobacilli are adapted to the URT and could have a beneficial keystone function in this habitat.

Identification and Monitoring of Lactobacillus delbrueckii Subspecies Using Pangenomic-Based Novel Genetic Markers

Genetic markers currently used for the discrimination of Lactobacillus delbrueckii subspecies have low efficiency for identification at subspecies level. Therefore, our objective in this study was to select novel genetic markers for accurate identification and discrimination of six L. delbrueckii subspecies based on pangenome analysis. We evaluated L. delbrueckii genomes to avoid making incorrect conclusions in the process of selecting genetic markers due to mislabeled genomes. Genome analysis showed that two genomes of L. delbrueckii subspecies deposited at NCBI were misidentified. Based on these results, subspecies-specific genetic markers were selected by comparing the core and pangenomes. Genetic markers were confirmed to be specific for 59,196,562 genome sequences via in silico analysis. They were found in all strains of the same subspecies, but not in other subspecies or bacterial strains. These genetic markers also could be used to accurately identify genomes at the subspecies level for genomes known at the species level. A real-time PCR method for detecting three main subspecies (L. delbrueckii subsp. delbrueckii, lactis, and bulgaricus) was developed to cost-effectively identify them using genetic markers. Results showed 100% specificity for each subspecies. These genetic markers could differentiate each subspecies from 44 other lactic acid bacteria. This real-time PCR method was then applied to monitor 26 probiotics and dairy products. It was also used to identify 64 unknown strains isolated from raw milk samples and dairy products. Results confirmed that unknown isolates and subspecies contained in the product could be accurately identified using this real-time PCR method.

Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis

Background

Bactrocera dorsalis is a destructive polyphagous and highly invasive insect pest of tropical and subtropical species of fruit and vegetable crops. The sterile insect technique (SIT) has been used for decades to control insect pests of agricultural, veterinary, and human health importance. Irradiation of pupae in SIT can reduce the ecological fitness of the sterile insects. Our previous study has shown that a gut bacterial strain BD177 that could restore ecological fitness by promoting host food intake and metabolic activities.

Results

Using long-read sequence technologies, we assembled the complete genome of K. michiganensis BD177 strain. The complete genome of K. michiganensis BD177 comprises one circular chromosome and four plasmids with a GC content of 55.03%. The pan-genome analysis was performed on 119 genomes (strain BD177 genome and 118 out of 128 published Klebsiella sp. genomes since ten were discarded). The pan-genome includes a total of 49305 gene clusters, a small number of 858 core genes, and a high number of accessory (10566) genes. Pan-genome and average nucleotide identity (ANI) analysis showed that BD177 is more similar to the type strain K. michiganensis DSM2544, while away from the type strain K. oxytoca ATCC13182. Comparative genome analysis with 21 K. oxytoca and 12 K. michiganensis strains, identified 213 unique genes, several of them related to amino acid metabolism, metabolism of cofactors and vitamins, and xenobiotics biodegradation and metabolism in BD177 genome.

Conclusions

Phylogenomics analysis reclassified strain BD177 as a member of the species K. michiganensis. Comparative genome analysis suggested that K. michiganensis BD177 has the strain-specific ability to provide three essential amino acids (phenylalanine, tryptophan and methionine) and two vitamins B (folate and riboflavin) to B. dorsalis. The clear classification status of BD177 strain and identification of unique genetic characteristics may contribute to expanding our understanding of the symbiotic relationship of gut microbiota and B. dorsalis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-020-00945-0.

Probiotic nasal spray development by spray drying

The upper respiratory tract (URT) is the main entrance point for many viral and bacterial pathogens, and URT infections are among the most common infections in the world. Recent evidences by our own group and others imply the importance of lactobacilli as gatekeepers of a healthy URT. However, the benefits of putting health-promoting microbes or potential probiotics, such as these URT lactobacilli, in function of URT disease control and prevention is underestimated, among others because of the absence of adequate formulation modalities. Therefore, this study entails important aspects in probiotic nasal spray development with a novel URT-derived probiotic strain by spray drying. We report quantitative and qualitative analysis of several spray-dried formulations, i.e. powders for reconstitution, based on disaccharide or sugar alcohol combinations with a polymer, including their long-term stability. Four formulations with the highest survival of >10⁹ (Colony Forming Units) CFU/g after 28 weeks were further examined upon reconstitution which confirmed sufficiency of one bottle/dosage form during 7 days and rheological properties of shear-thinning. Tests also demonstrated maintained viability and cell morphology overall upon spraying through a nasal spray bottle in all 4 formulations. Lastly, application suitability in terms of high adherence to Calu-3 cells and antimicrobial activity against common URT pathogens was demonstrated and was not impacted neither by powder production process nor by spraying of reconstituted powder through a nasal spray device.

Selection of Immunobiotic Ligilactobacillus salivarius Strains from the Intestinal Tract of Wakame-Fed Pigs: Functional and Genomic Studies

In this article, Ligilactobacillus salivarius FFIG strains, isolated from the intestinal tract of wakame-fed pigs, are characterized according to their potential probiotic properties. Strains were evaluated by studying their interaction with porcine intestinal epithelial (PIE) cells in terms of their ability to regulate toll-like receptor (TLR)-3- or TLR4-mediated innate immune responses, as well as by assessing their adhesion capabilities to porcine epithelial cells and mucins. These functional studies were complemented with comparative genomic evaluations using the complete genome sequences of porcine L. salivarius strains selected from subgroups that demonstrated different “immune” and “adhesion” phenotypes. We found that their immunomodulatory and adhesion capabilities are a strain-dependent characteristic. Our analysis indicated that the differential immunomodulatory and adhesive activities of FFIG strains would be dependent on the combination of several surface structures acting simultaneously, which include peptidoglycan, exopolysaccharides, lipoteichoic acid, and adhesins. Of note, our results indicate that there is no correlation between the immunomodulatory capacity of the strains with their adhesion ability to mucins and epithelial cells. Therefore, in the selection of strains destined to colonize the intestinal mucosa and modulate the immunity of the host, both properties must be adequately evaluated. Interestingly, we showed that L. salivarius FFIG58 functionally modulated the innate immune responses triggered by TLR3 and TLR4 activation in PIE cells and efficiently adhered to these cells. Moreover, the FFIG58 strain was capable of reducing rotavirus replication in PIE cells. Therefore, L. salivarius FFIG58 is a good candidate for further in vivo studying the protective effect of lactobacilli against intestinal infections in the porcine host. We also reported and analyzed, for the first time, the complete genome of several L. salivarius strains that were isolated from the intestine of pigs after the selective pressure of feeding the animals with wakame. Further genomic analysis could be of value to reveal the metabolic characteristics and potential of the FFIG strains in general and of the FFIG58 strain, in particular, relating to wakame by-products assimilation.

The role of probiotics on the roadmap to a healthy microbiota: a symposium report

The ninth International Yakult Symposium was held in Ghent, Belgium in April 2018. Keynote lectures were from Professor Wijmenga on using biobanks to understand the relationship between the gut microbiota and health; and Professor Hill on phage-probiotic interactions. Session one included talks from Professor Plӧsch on epigenetic programming by nutritional and environmental factors; Professor Wilmes on the use of "omics" methodologies in microbiome research and Professor Rescigno on the gut vascular barrier. Session two explored the evidence behind Lactobacillus casei Shirota with Dr Nanno explaining the plasticity in immunomodulation that enables the strain to balance immune functions; Dr Macnaughtan outlining its potential therapeutic use in cirrhosis and Professor Nishida detailing effects in subjects under stress. The third session saw Professor Marchesi describing that both the host genes and the gut microbiota can play a role in cancer; Professor Bergheim highlighting crosstalk between the gut and the liver and Professor Cani describing the relationship between the gut microbiota and the endocrine system. The final session explored probiotic mechanisms, with Professor Lebeer dissecting the challenges in conducting mechanistic studies; Professor Wehkamp describing the mucosal defence system and Professor Van de Wiele detailing methods for modelling the gut microbiota in vitro.

Strain-specific differences in behaviour among Lacticaseibacillus rhamnosus cell wall mutants during direct compression

The human body harbours a large variety of microbial communities. It is already well-known that these communities play an important role in human health. Therefore, microbial imbalances can be responsible for several health disorders by different mechanisms. In recent years, probiotic bacteria have been increasingly applied to restore imbalances and stimulate microbiome functions such as immune modulation. Tablets are the dosage form of choice for oral probiotics. Nevertheless, a probiotic tablet with a sufficient amount of viable cells remains a challenge due to the stress of the compression process. Recent research demonstrated that the applied pressure and tableting properties play an important role in the survival of Lacticaseibacillus rhamnosus GG during direct compression. This study focused on the importance of the cell surface molecules in the protection of this prototype probiotic strain during direct compression. Spray-dried powders of L. rhamnosus GG and its exopolysaccharide-deficient mutant and lipoteichoic acid mutant were blended with two different filler-binders and compacted at various compression pressures. Under each tableting condition, the survival rate and tableting properties were analysed. The results demonstrated that the cell surface molecules play an important role in the behaviour of L. rhamnosus GG during direct compression. Specifically, the long, galactose-rich exopolysaccharides of L. rhamnosus served a protective shield during tablet production, promoting the survival rate of this probiotic strain. The D-alanylation of the lipoteichoic acids plays also an important role. When the D-alanyl ester content was completely absent, the survival rate was less affected by the tableting properties. Moreover, this research revealed that the sensitivity to the tableting properties is species and strain dependent.

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.

Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

Taxonomic relationships between Lactobacillus casei , Lactobacillus paracasei and Lactobacillus zeae have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains L. casei ATCC 393T and L. zeae ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that L. casei could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the L. zeae strains, and supported an emended the description of the name of Lactobacillus zeae (ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level

The genus Lactobacillus includes, among others, Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus, species that are collectively referred to as the Lactobacillus casei group. Many studies have shown that strains belonging to this group may decrease lactose intolerance, the effects of inflammatory bowel disease, diarrhea, constipation, food allergies and even colon cancer. Moreover, evidences exists of positive effects of these bacteria on mucosal immunity and blood cholesterol level. Because of their beneficial influence on human health, many of them are used as food additives and probiotic pharmaceuticals. It should be stressed that health-promoting properties are not attributed at the species level, but to specific strains. Therefore, procedures are necessary to allow specific identification at each phylogenetic level-genus, species and strain. In this paper we present a practical overview of molecular methods for the identification and differentiation of L. casei bacteria. The research included 30 bacterial strains belonging to three species: L.casei, L. paracasei and L. rhamnosus. Among the tested procedures were genus- and species-specific PCR, multiplex-PCR, Real-Time HRM analysis, RFLP-PCR, rep-PCR, RAPD-PCR, AFLP-PCR, and proteomic methods such as MALDI-TOF MS typing and SDS-PAGE fingerprinting. The obtained results showed that multiplex-PCR and MALDI-TOF MS turned out to be the most useful methods to identify the tested bacteria at the species level. At the strain level, the AFLP-PCR method showed the highest discriminatory power. We hope that the presented results will allow for the easy selection of an appropriate procedure, depending on the experiment conducted and the equipment capabilities of any given laboratory.

Prolonged Heat Stress of Lactobacillus paracasei GCRL163 Improves Binding to Human Colorectal Adenocarcinoma HT-29 Cells and Modulates the Relative Abundance of Secreted and Cell Surface-Located Proteins

Lactobacillus casei group bacteria improve cheese ripening and may interact with host intestinal cells as probiotics, where surface proteins play a key role. Three complementary methods [trypsin shaving (TS), LiCl-sucrose (LS) extraction, and extracellular culture fluid precipitation] were used to analyze cell surface proteins of Lactobacillus paracasei GCRL163 by label-free quantitative proteomics after culture to the mid-exponential phase in bioreactors at pH 6.5 and temperatures of 30-45 °C. A total of 416 proteins, including 300 with transmembrane, cell wall anchoring, and secretory motifs and 116 cytoplasmic proteins, were quantified as surface proteins. Although LS caused significantly greater cell lysis as growth temperature increased, higher numbers of extracytoplasmic proteins were exclusively obtained by LS treatment. Together with the increased positive surface charge of cells cultured at supra-optimal temperatures, proteins including cell wall hydrolases Msp1/p75 and Msp2/p40, α-fucosidase AlfB, SecA, and a PspC-domain putative adhesin were upregulated in surface or secreted protein fractions, suggesting that cell adhesion may be altered. Prolonged heat stress (PHS) increased binding of L. paracasei GCRL163 to human colorectal adenocarcinoma HT-29 cells, relative to acid-stressed cells. This study demonstrates that PHS influences cell adhesion and relative abundance of proteins located on the surface, which may impact probiotic functionality, and the detected novel surface proteins likely linked to the cell cycle and envelope stress.

Plant pangenomics: approaches, applications and advancements

With the assembly of increasing numbers of plant genomes, it is becoming accepted that a single reference assembly does not reflect the gene diversity of a species. The production of pangenomes, which reflect the structural variation and polymorphisms in genomes, enables in depth comparisons of variation within species or higher taxonomic groups. In this review, we discuss the current and emerging approaches for pangenome assembly, analysis and visualisation. In addition, we consider the potential of pangenomes for applied crop improvement, evolutionary and biodiversity studies. To fully exploit the value of pangenomes it is important to integrate broad information such as phenotypic, environmental, and expression data to gain insights into the role of variable regions within genomes.

Novel real-time PCR assay for Lactobacillus casei group species using comparative genomics

The Lactobacillus casei group, which includes the closely related species L. casei, L. paracasei, L. rhamnosus, and L. chiayiensis, has been under debate regarding its taxonomy because of the difficulty in distinguishing the species from each other. In the present study, we developed a novel real-time PCR assay for distinguishing the L. casei group species. The pan-genome, as determined by the genomes of 44 strains, comprised 6789 genes, comparative genomic analysis showed that L. casei group strains were classified by species. Based on these results, species-specific genes were identified, and primers were designed from those genes. Real-time PCR clearly distinguished each species of the L. casei group and specifically amplified only to the target species. The method was applied to 29 probiotic products, and the detected results and label claims were compared. Total 23 products were in accordance with the label claims, and the remaining products contained species different from those stated in the label claims. Our method can rapidly and accurately distinguish the L. casei group species in a single reaction. Hence, our assay can be applied to identify L. casei group species from food or environmental samples and to accurately determine the nomenclature of the species.

Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen

Lactobacillus rhamnosus Pen is a human endogenous strain used for the production of probiotic formula, which is effective in the prevention of antibiotic-associated diarrhoea. Our study showed that this probiotic strain releases bacteriophage BH1 without the addition of any inducing agent. Our research revealed that phage BH1 has a circular genome with a length of 40721 nt and a GC content of 44.8%. The genome of phage BH1 possesses 57 open reading frames which could be divided into functional modules associated with DNA packaging, morphogenesis, lysis, integration, genetic switch, and replication. In spite of similarity in morphology and genomic organization, comparative analysis revealed substantial genetic diversity and mosaic genomic architecture among phages described for the Lactobacillus casei group. Additionally, qPCR and ddPCR analysis confirmed earlier microscopic observations indicating that L. rhamnosus Pen liberates bacteriophage particles during growth. This occurs spontaneously, and is not a result of external inducing factors. For samples collected after 4 and 24 h of L. rhamnosus Pen culture, the number of attB and attP copies increased 2.5 and 12 times, respectively. This phenomenon, by introducing resistance to other phages or enhancing the biofilm-forming capabilities, may increase the survivability of microorganisms in their natural ecological niche. Conversely, spontaneous phage induction may be an important virulence factor for bacteria, posing a potential threat for the human host.

Applications of plant-based fermented foods and their microbes

Plant-based fermentations and their microbes provide an underexplored source for novel biotechnological applications. Recent advances in DNA sequencing technologies and analyses of sequencing data highlight that a diverse array of lactic acid bacteria (LAB) frequently dominate these plant fermentations. Because of the long history of safe LAB use in fermented foods, we argue here that various novel probiotic, synbiotic and a range of other industrial applications can be produced based on new insights in the functional and genetic potential of these LAB. To aid in this quest, comparative genomics tools are increasingly available enabling a more rational design of wet-lab experiments to screen for the most relevant properties. This is also true for the exploration of useful enzymatic and (secondary) metabolic production capacities of the LAB that can be isolated from these plant-based fermentations, such as the recent discovery of a cellulase enzyme in specific Lactobacillus plantarum group members.

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.

Translating Recent Microbiome Insights in Otitis Media into Probiotic Strategies

The microbiota of the upper respiratory tract (URT) protects the host from bacterial pathogenic colonization by competing for adherence to epithelial cells and by immune response regulation that includes the activation of antimicrobial and (anti-)inflammatory components. However, environmental or host factors can modify the microbiota to an unstable community that predisposes the host to infection or inflammation. One of the URT diseases most often encountered in children is otitis media (OM). The role of pathogenic bacteria like Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in the pathogenesis of OM is well documented. Results from next-generation-sequencing (NGS) studies reveal other bacterial taxa involved in OM, such as Turicella and Alloiococcus Such studies can also identify bacterial taxa that are potentially protective against URT infections, whose beneficial action needs to be substantiated in relevant experimental models and clinical trials. Of note, lactic acid bacteria (LAB) are members of the URT microbiota and associated with a URT ecosystem that is deemed healthy, based on NGS and some experimental and clinical studies. These observations have formed the basis of this review, in which we describe the current knowledge of the molecular and clinical potential of LAB in the URT, which is currently underexplored in microbiome and probiotic research.

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.