Screening of Lactobacillus salivarius strains from the feces of Chinese populations and the evaluation of their effects against intestinal inflammation in mice

The protective effects of Lactobacillus SNK-6 on growth, organ health, and intestinal function in geese exposed to low concentration Aflatoxin B1

Aflatoxin B1 (AFB1) is a prevalent mycotoxin present in feed ingredients. In this study, we investigated the effects of Lactobacillus salivarius (L. salivarius) on the Landes geese exposed to AFB1. The 300 one-day-old Landes geese were randomly divided into five groups: The control group received a basic diet, while the other groups were fed a basic diet supplemented with 10 μg/kg AFB1, 10 μg/kg AFB1+ 4*108 cfu/g L. salivarius, 50 μg/kg AFB1, and 50 μg/kg AFB1 + 4*108 cfu/g L. salivarius for 63 d. Results showed that high level AFB1 exposure significantly decreased final BW and ADG, increased feed/gain ratio (F/G) and liver index (P < 0.05). L. salivarius improved levels of IL-1, IL-6, and IL-12 under low level of AFB1 exposure (P < 0.05), along with similar trends observed in serum IgA, IgG, IgM, T3, T4, TNF-ɑ, and EDT (P < 0.05). AFB1 exposure reduced jejunum villus high and villus high/crypt depth ratio, and suppressed expression of ZO-1, Occludin, and Claudin-1 mRNA, and significant improved with L. salivarius supplementation under low level AFB1 exposure (P < 0.05). AFB1 significantly increased expression levels of TLR3 and NF-kB1, with supplementation of L. salivarius showing significant improvement under low AFB1 exposure (P < 0.05). Cecal microbiota sequencing revealed that under low level AFB1 exposure, supplementation with L. salivarius increased the abundance of Bacteroidetes and Lactococcus. In summary, supplementation with 4*108 cfu/g L. salivarius under 10 μg/kg AFB1 exposure improved growth performance and immune capacity, enhanced jejunum morphology, reduced liver inflammation, altered the cecal microbial structure, and positively affected the growth and development of geese.

Metabolomic analysis reveals Ligilactobacillus salivarius CCFM 1266 fermentation improves dairy product quality

Previous studies have demonstrated that Ligilactobacillus salivarius CCFM 1266 exhibits anti-inflammatory properties and the capability to synthesize niacin. This study aimed to investigate the fermentative abilities of L. salivarius CCFM 1266 in fermented milk. Metabonomic analysis revealed that fermentation by L. salivarius CCFM 1266 altered volatile flavor compounds and metabolite profiles, including heptanal, nonanal, and increased niacin production. Genomic investigations confirmed that L. salivarius CCFM 1266 possess essential genes for the metabolism of fructose and mannose, affirming its proficiency in utilizing fructooligosaccharides and mannan oligosaccharides. The addition of fructooligosaccharides and mannan oligosaccharides during the fermentation process significantly facilitated the proliferation of L. salivarius CCFM 1266 in fermented milk, with growth exceeding 107 colony-forming units (CFU)/mL. This intervention not only augmented the microbial density but also modified the metabolite composition of fermented milk, resulting in an elevated presence of advantageous flavor compounds such as nonanal, 2,3-pentanedione, and 3-methyl-2-butanone. However, its influence on improving the texture of fermented milk was observed to be minimal. Co-fermentation of L. salivarius CCFM 1266 with commercial fermentation starters indicated that L. salivarius CCFM 1266 was compatible, similarly altering metabolite composition and increasing niacin content in fermented milk. In summary, the findings suggest that L. salivarius CCFM 1266 holds substantial promise as an adjunctive fermentation starter, capable of enhancing the nutritional diversity of fermented milk products.

Analysis of the key genes of Lactobacillus reuteri strains involved in the protection against alcohol-induced intestinal barrier damage

Gastrointestinal inflammation and intestinal barrier function have important effects on human health. Alcohol, an important foodborne hazard factor, damages the intestinal barrier, increasing the risk of disease. Lactobacillus reuteri strains have been reported to reduce gastrointestinal inflammation and strengthen the intestinal barrier. In this study, we selected three anti-inflammatory L. reuteri strains to evaluate their role in the protection of the intestinal barrier and their immunomodulatory activity in a mouse model of gradient alcohol intake. Among the three strains tested (FSCDJY33M3, FGSZY33L6, and FCQHCL8L6), L. reuteri FSCDJY33M3 was found to protect the intestinal barrier most effectively, possibly due to its ability to reduce the expression of interleukin (IL)-1β, IL-6, and tumor necrosis factor-alpha (TNF-α) and increase the expression of tight junction proteins (occludin, claudin-3). Genomic analysis suggested that the protective effects of L. reuteri FSCDJY33M3 may be related to functional genes and glycoside hydrolases associated with energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, and DNA replication, recombination, and repair. These genes include COG2856, COG1804, COG2071, and COG1061, which encode adenine deaminase, acyl-CoA transferases, glutamine amidotransferase, RNA helicase, and glycoside hydrolases, including GH13_20, GH53, and GH70. Our results identified functional genes that may be related to protection against alcohol-induced intestinal barrier damage, which might be useful for screening lactic acid bacterial strains that can protect the intestinal barrier.

Ligilactobacillus salivarius CCFM 1266 modulates gut microbiota and GPR109a-mediated immune suppression to attenuate immune checkpoint blockade-induced colitis

The wide application of immune checkpoint blockade (ICB) therapy is impeded by the development of ICB-induced colitis, a condition intricately linked to alterations in the gut microbiota. In our previous study, Ligilactobacillus salivarius CCFM 1266 and Bacteroides fragilis HCK-B3 exhibited anti-inflammatory properties. In this research, treatment with both L. salivarius CCFM 1266 and B. fragilis HCK-B3 significantly ameliorated body weight loss and colonic inflammation in murine colitis models induced by intravenous ipilimumab injection, with L. salivarius CCFM 1266 demonstrating superior effectiveness. This amelioration was characterized by an augmented ratio of Treg cells and M2 macrophages, a diminishment in pro-inflammatory cytokines (IL-1β, TNF-α, IFN-γ, IL-23), and an elevation in the anti-inflammatory cytokine IL-10. The ingestion of L. salivarius CCFM 1266 exerted a discernible influence on the composition of the gut microbiota. Untargeted metabolomics revealed an increase in colonic nicotinic acid levels following the administration of L. salivarius CCFM 1266, potentially initiating the activation of the colonic GPR109a pathway. This mechanism likely serves as the fundamental basis for the protective capacity of L. salivarius CCFM 1266 against ICB-induced colitis. Importantly, L. salivarius CCFM 1266 did not interfere with the anti-tumor immune response elicited by ipilimumab. Probiotic intervention thus emerges as a promising approach for alleviating ICB-induced colitis.

Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers

BACKGROUND

Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a "generalist" species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive.

RESULTS

In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events.

CONCLUSIONS

A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers' gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.

Lactobacillus salivarius WZ1 Inhibits the Inflammatory Injury of Mouse Jejunum Caused by Enterotoxigenic Escherichia coli K88 by Regulating the TLR4/NF-κB/MyD88 Inflammatory Pathway and Gut Microbiota

Replacing antibiotics with probiotics has become an important way to safely and effectively prevent and treat some gastrointestinal diseases. This study was conducted to investigate whether Lactobacillus salivarius WZ1 (L.S) could reduce the inflammatory injury to the mouse jejunum induced by Escherichia coli (ETEC) K88. Forty Kunming mice were randomly divided into four groups with 10 mice in each group. From day 1 to day 14, the control group and the E. coli group were administered with normal saline each day, while the L.S group and the L.S + E. coli group were gavaged with Lactobacillus salivarius WZ1 1 × 108 CFU/mL each day. On the 15th day, the E. coli group and the L.S + E. coli group were intragastrically administered ETEC K88 1 × 109 CFU/mL and sacrificed 24 h later. Our results show that pretreatment with Lactobacillus salivarius WZ1 can dramatically protect the jejunum morphological structure from the changes caused by ETEC K88 and relieve the morphological lesions of the jejunum, inhibiting changes in the mRNA expressions of TNF-α, IL-1β and IL-6 and the protein expressions of TLR4, NF-κB and MyD88 in the intestinal tissue of mice caused by ETEC K88. Moreover, pretreatment with Lactobacillus salivarius WZ1 also increased the relative abundance of beneficial genera such as Lactobacillus and Bifidobacterium and decreased the abundance of harmful genera such as Ralstonia and Helicobacter in the gut. These results demonstrate that Lactobacillus salivarius WZ1 can inhibit the inflammatory damage caused by ETEC K88 in mouse jejunum by regulating the TLR4/NF-κB/MyD88 inflammatory pathway and gut microbiota.

Lactobacillus reuteri normalizes altered fear memory in male Cntnap4 knockout mice

BACKGROUND

Autism spectrum disorder (ASD) is a common neurodevelopmental disease, characterized by deficits in social communication, restricted and repetitive behaviours, and impaired fear memory processing. Severe gastrointestinal dysfunction and altered gut microbiome have been reported in ASD patients and animal models. Contactin associated protein-like 4 (CNTNAP4) has been suggested to be a novel risk gene, though its role in ASD remains unelucidated.

METHODS

Cntnap4^-/- mice were generated to explore its role in ASD-related behavioural abnormalities. Electrophysiological recording was employed to examine GABAergic transmission in the basolateral amygdala (BLA) and prefrontal cortex. RNA-sequencing was performed to assess underlying mechanisms. 16S rDNA analysis was performed to explore changes in faecal microbial composition. Male Cntnap4^-/- mice were fed with Lactobacillus reuteri (L. reuteri) or faecal microbiota to evaluate the effects of microbiota supplementation on the impaired fear conditioning mediated by Cntnap4 deficiency.

FINDINGS

Male Cntnap4^-/- mice manifested deficiency in social behaviours and tone-cue fear conditioning. Notably, reduced GABAergic transmission and GABA receptor expression were found in the BLA but not the prefrontal cortex. In addition, gut Lactobacillus were less abundant in male Cntnap4^-/- mice, and L. reuteri treatment or faecal microbiota transplantation rescued abnormal tone-cued fear memory and improved local GABAergic transmission in the BLA of male Cntnap4^-/- mice.

INTERPRETATION

Cntnap4 shapes GABAergic transmission of amygdala and fear conditioning, and microbial intervention represents a promising therapy in ASD intervention.

FUNDING

National Natural Science Foundation of China, Science and Technology Planning Project of Guangzhou, Guangzhou Medical University, and China Postdoctoral Science Foundation.

Complete Genome Sequence of Lactobacillus salivarius AR809, a Probiotic Strain with Oropharyngeal Tract Resistance and Adhesion to the Oral Epithelial Cells

Lactobacillus salivarius AR809 was isolated from a healthy adult oral cavity with multiple probiotic properties, such as high antimicrobial activity, adhesion to the oral epithelium, resistance to acidic pH, bile, lysozyme, and H₂O₂. In this study, to investigate the genetic basis on probiotic potential and identify the functional genes in the strain, the complete genome of strain AR809 was sequenced by Illumina and PacBio platforms. Then comparative genome analysis on 11 strains of Lactobacillus salivarius was performed. The complete genome of AR809 consisted of a circular 1,747,224 bp chromosome with 33.00% GC content and four circular plasmids [pA (247,948 bp), pB (27,292 bp), pC (3349 bp), and pD (2898 bp), respectively]. From among the 1866 protein-coding genes, 130 carbohydrate metabolism-related genes, 18 bacteriocin biosynthesis-related genes, 74 environmental stress-related genes, and a series of adhesion-related genes were identified via clusters of orthologous genes, Koyto Encyclopedia of Genes and Genomes, and carbohydrate-active enzymes annotation. The comparative genome analysis indicated that genomic homology between AR809 and CICC23174 was the highest. In conclusion, the present work provided valuable insights into the gene's function prediction and understanding the genetic basis on adapting to host oropharyngeal-gastrointestinal tract in strain AR809.

Novel Probiotic Lactic Acid Bacteria Were Identified from Healthy Infant Feces and Exhibited Anti-Inflammatory Capacities

The current study aims to evaluate the probiotic potential of lactic acid bacteria isolated from infant feces, and select candidates to be used as potential antioxidants for the treatment of oxidative stress-related diseases; To meet the criteria for probiotic attributes, the isolates were subjected to various in vitro tests and 16S rRNA genotypic characterization. Besides, anti-inflammatory and anti-oxidative effects of selected isolates were separately assessed by real-time quantitative PCR and Western blot; The selected strains belonged to Lactobacillus gasseri, Lactiplantibacillus plantarum and Lacticaseibacillus rhamnosus. Notably, three selected strains (L. gasseri FWJL-4, L. plantarum Fjias-5 and L. rhamnosus FSJ-13) particularly L. gasseri FWJL-4 significantly down-regulated mRNA expression levels of tumor necrosis factor α (TNFα), Interleukin-6 (IL-6) and IL-1β. Most importantly, three strains-treated RAW 264.7 murine macrophages displayed enhanced activities of antioxidant enzymes and reduced H₂O₂ production, which were associated with the enhanced expression levels of nuclear factor-erythroid 2 related factor 2 and heme oxygenase-1; Three selected strains, particularly L. gasseri FWJL-4, are good candidates that merit additional in vivo investigation for the validation and application of their health-promoting effects.

Lactobacillus salivarius CML352 Isolated from Chinese Local Breed Chicken Modulates the Gut Microbiota and Improves Intestinal Health and Egg Quality in Late-Phase Laying Hens

Lactobacillus strains with fine probiotic properties are continuously needed in the laying hen industry to improve the animals’ gut health and production performance. In this study, we isolated 57 Lactobacillus strains from the gut microbiota of 17 different chicken breeds in China. We characterized the probiotic features of these isolates, and evaluated the effects of a selected strain, Lactobacillus salivarius CML352, on the production performance and gut health of the late-phase laying hens. The results showed that the isolates varied much in probiotic properties, among which L. salivarius CML352 displayed high acid and bile salt tolerance, high hydrophobicity, auto-aggregation, and antibacterial activities. Whole genome sequencing analysis showed that CML352 was closely related to a strain isolated from human fecal samples, but had different functional potentials. Dietary supplementary of L. salivarius CML352 significantly reduced the Firmicutes to Bacteroidetes ratio, increased the expression of Muc-2, and decreased the expression of MyD88, IFN-γ, and TLR-4. Furthermore, strain CML352 reduced the birds’ abdominal fat deposition, and improved egg quality. Taken together, this study indicated that the newly isolated L. salivarius strain might be a worthy probiotic with positive impacts on the intestinal health and production performance of late-phase laying hens.

Protective effects of Bacteroides fragilis against lipopolysaccharide-induced systemic inflammation and their potential functional genes

Bacteroides fragilis, one of the potential next-generation probiotics, has been demonstrated to alleviate inflammation-associated diseases. In this study, we compare the anti-inflammatory effects of six Bacteroides fragilis strains on systemic inflammation and link their strain-specific characteristics, both physiologically and genetically, to their function. A lipopolysaccharide (LPS)-induced systemic inflammation model in mice was used as an in vivo model to compare the effects of different B. fragilis strains. Short-chain fatty acids (SCFAs) were measured by gas chromatography-mass spectrometry (GC-MS). The in vitro immunomodulatory properties were evaluated in LPS-stimulating RAW264.7 cell lines. Orthologous gene clusters were compared using OrthoVenn2. The results indicate a strain-specific in vitro anti-inflammatory effect. Effective strains induce higher colon SCFAs in vivo and interleukin-10 (IL-10) production in vitro. Comparative genomic analysis showed that the SCFA-inducing strains possess three genes relating to carbohydrate metabolism (GH2, GH35 families) and binding and transportation (SusD), all of which are associated with niche fitness and expansion. IL-10-inducing strains share a highly similar gene, wbjE, which may result in a distinct O-antigen structure of LPS and influence their immunomodulatory properties. B. fragilis is strain-specific against LPS-induced systemic inflammation in mice. The beneficial effects of a specific strain may be attributed to its SCFA and IL-10 inducing abilities. Strain-specific potential genes can be excavated to link these differences.

Microbiota-targeted therapies in inflammation resolution

Gut microbiota has been shown to systemically shape the immunological landscape, modulate homeostasis and play a role in both health and disease. Dysbiosis of gut microbiota promotes inflammation and contributes to the pathogenesis of several major disorders in gastrointestinal tract, metabolic, neurological and respiratory diseases. Much effort is now focused on understanding host-microbes interactions and new microbiota-targeted therapies are deeply investigated as a means to restore health or prevent disease. This review details the immunoregulatory role of the gut microbiota in health and disease and discusses the most recent strategies in manipulating individual patient's microbiota for the management and prevention of inflammatory conditions.

Formononetin reshapes the gut microbiota, prevents progression of obesity and improves host metabolism

Formononetin (FMNT) is an isoflavone that has been studied for its anti-hyperglycemic and anti-diabetic effects. However, the effect of FMNT on gut dysbiosis and metabolic complications associated with western-style diet consumption has not been reported yet. This study aimed to investigate how FMNT can reshape the gut microbiota at a specific dosage and ameliorate the symptoms of obesity-related metabolic disorders in both genders. Results indicate that FMNT at 60 mg per kg bodyweight dosage can effectively control body weight, hyperglycemia, and insulin resistance, leptin levels and improve HDL to LDL ratio. FMNT treatment suppressed Porphyromonadaceae (Uncultured Alistipes) and augmented maximum genera from families Lachnospiraceae and Clostridiacea, but at species level, formononetin increased Clostridium aldenense, Clostridiaceae unclassified, Eubacterium plexicaum; acetate and butyrate-producing bacteria. Moreover, formononetin regulated the expression of specific liver miRNA involved in obesity and down-regulated mRNA expression levels of pro-inflammatory cytokines IL-6, IL-22 and TNF-α. Additionally, FMNT maintained intestinal membrane integrity by regulating the expression of Muc-2 and occludin. Our findings indicate that FMNT could be a potential prebiotic that can effectively regulate the gut microbiota, improve host metabolism and systemic inflammation, and prevent deleterious effects of a western-style diet by elevating acetate lactate and lactate butyrate producers.

Ligilactobacillus salivarius functionalities, applications, and manufacturing challenges

Ligilactobacillus salivarius is a lactic acid bacteria that has been gaining attention as a promising probiotic. Numerous strains exhibit functional properties with health benefits such as antimicrobial activity, immunological effects, and the ability to modulate the intestinal microbiota. However, just a small number of them are manufactured at an industrial scale and included in commercial products. The under exploitation of L. salivarius strains that remain in the freezer of companies is due to their incapacity to overcome the environmental stresses induced by production and stabilization processes.The present study summarizes the functionalities and applications of L. salivarius reported to date. It aims also at providing a critical evaluation of the literature available on the manufacturing steps of L. salivarius concentrates, the bacterial quality after each step of the process, and the putative degradation and preservation mechanisms. Here, we highlight the principal issues and future research challenges for improving the production and long-term preservation at the industrial scale of this microorganism, and probably of other probiotics.Key points• L. salivarius beneficial properties and commercialized products.• Production conditions and viability of L. salivarius after stabilization processes.• Prospects for identifying preservation mechanisms to improve L. salivarius stability.

Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius

Lactobacillus salivarius has drawn attention because of its promising probiotic functions. Tolerance to the gastrointestinal tract condition is crucial for orally administrated probiotics to exert their functions. However, previous studies of L. salivarius have only focused on the bile salt resistance of particular strains, without uncovering the common molecular mechanisms of this species. Therefore, in this study, we expanded our research to 90 L. salivarius strains to explore their common functional genes for bile salt resistance. First, the survival rates of the 90 L. salivarius strains in 0.3% bile salt solutions were determined. Comparative genomics analysis was then performed to screen for the potential functional genes related to bile salt tolerance. Next, real-time polymerase chain reaction and gene knockout experiments were conducted to further verify the tolerance-related functional genes. The results indicated that the strain-dependent bile salt tolerance of L. salivarius was mainly associated with four peptidoglycan synthesis-related genes, seven phosphotransferase system-related genes, and one chaperone-encoding gene involved in the stress response. Among them, the GATase1-encoding gene showed the most significant association with bile salt tolerance. In addition, four genes related to DNA damage repair and substance transport were redundant in the strains with high bile salt tolerance. Besides, cluster analysis showed that bile salt hydrolases did not contribute to the bile salt tolerance of L. salivarius. In this study, we determined the global regulatory genes, including LSL_1568, LSL_1716 and LSL_1709, for bile salt tolerance in L. salivarius and provided a potential method for the rapid screening of bile salt-tolerant L. salivarius strains, based on PCR amplification of functional genes.

Screening beneficial bacteriostatic lactic acid bacteria in the intestine and studies of bacteriostatic substances

Lactic acid bacteria (LAB) are a representative probiotic. As the dominant flora in the human intestinal tract, LAB can regulate the balance of human intestinal flora and improve host health. The purpose of this study was to isolate and screen LAB that are well suited to the intestinal characteristics of the Chinese population, with excellent probiotics and high antibacterial activity. After 16S ribosomal RNA (rRNA) homology and phylogenetic tree analysis, potential probiotics were tested for their antibacterial activity, resistance to artificial gastrointestinal fluid and drugs, surface hydrophobicity, and safety. Three strains of LAB with acid resistance, bile salt resistance, epithelial cell adhesion, and no multidrug resistance were selected: Lactobacillus salivarius, Leuconostoc lactis, and Lactobacillus paracasei. Analysis of the antibacterial active substances in the three strains and their fermentation broths revealed that the main antibacterial substances of L. lactis were organic acids, whereas those of L. salivarius and L. paracasei were organic acids and bacteriocins with broad-spectrum antibacterial activity. These three strains of probiotic LAB with high antibacterial activity were identified as bacterial resources that could potentially be used to develop probiotic preparations for the prevention and treatment of intestinal diseases caused by intestinal pathogens.

Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems

Prophage integration, release, and dissemination exert various effects on host bacteria. In the genus Lactobacillus, they may cause bacteriophage contamination during fermentation and even regulate bacterial populations in the gut. However, little is known about their distribution, genetic architecture, and relationships with their hosts. Here, we conducted prophage prediction analysis on 1,472 genomes from 16 different Lactobacillus species and found prophage fragments in almost all lactobacilli (99.8%), with 1,459 predicted intact prophages identified in 64.1% of the strains. We present an uneven prophage distribution among Lactobacillus species; multihabitat species retained more prophages in their genomes than restricted-habitat species. Characterization of the genome features, average nucleotide identity, and landscape visualization presented a high genome diversity of Lactobacillus prophages. We detected antibiotic resistance genes in more than 10% of Lactobacillus prophages and validated that the occurrence of resistance genes conferred by prophage integration was possibly associated with phenotypic resistance in Lactobacillus plantarum. Furthermore, our broad and comprehensive examination of the distribution of CRISPR-Cas systems across the genomes predicted type I and type III systems as potential antagonistic elements of Lactobacillus prophage.

IMPORTANCE Lactobacilli are inherent microorganisms in the human gut and are widely used in the food processing industries due to their probiotic properties. Prophages were reportedly hidden in numerous Lactobacillus genomes and can potentially contaminate entire batches of fermentation or modulate the intestinal microecology once they are released. Therefore, a comprehensive scanning of prophages in Lactobacillus is essential for the safety evaluation and application development of probiotic candidates. We show that prophages are widely distributed among lactobacilli; however, intact prophages are more common in multihabitat species and display wide variations in genome feature, integration site, and genomic organization. Our data of the prophage-mediated antibiotic resistance genes (ARGs) and the resistance phenotype of lactobacilli provide evidence for deciphering the putative role of prophages as vectors of the ARGs. Furthermore, understanding the association between prophages and CRISPR-Cas systems is crucial to appreciate the coevolution of phages and Lactobacillus.

Evaluation of the Effects of Different Bacteroides vulgatus Strains against DSS-Induced Colitis

Although the strain-dependent effects of Bacteroides vulgatus on alleviating intestinal inflammatory diseases have been demonstrated, the literature has rarely focused on the underlying causes of this effect. In this study, we selected four B. vulgatus strains (FTJS5K1, FTJS7K1, FSDTA11B14, and FSDLZ51K1) with different genomic characteristics and evaluated their protective roles against dextran sulfate sodium- (DSS-) induced colitis. Compared to the other three tested strains, B. vulgatus 7K1 more strongly ameliorated the DSS-induced weight loss, shortening of the colon length, increased disease activity index scores, colonic tissue injury, and immunomodulatory disorder. In contrast, B. vulgatus 51K1 significantly worsened the DSS-induced alterations in the tumor necrosis factor-alpha (TNF-α) concentration and colonic histopathology. A comparative genomic analysis of B. vulgatus 7K1 and 51K1 showed that the beneficial effects of B. vulgatus 7K1 may be associated with some of its specific genes involved in the production of short-chain fatty acids or capsular polysaccharides and enhancement of its survivability in the gut. In conclusion, these findings indicate that the supplementation of B. vulgatus 7K1 is a potentially efficacious intervention for alleviating colitis and provides scientific support for the screening of probiotics with anticolitis effect.

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.

Identification of the key characteristics of Bifidobacterium longum strains for the alleviation of ulcerative colitis

Bifidobacterium longum (B. longum) species are widely used to prevent and treat ulcerative colitis (UC). In this study, phylogenetic and pan-genomic characterization of 122 B. longum strains was performed on the basis of 936 core genes; among these, four strains from different branches of the phylogenetic tree were selected for an evaluation of anti-inflammatory and immune modulatory activities in a DSS-induced colitis mouse model. Among the tested B. longum strains (B. longum FBJ20M1, B. longum FGDLZ8M1, B. longum FGSZY16M3, and B. longum FJSWXJ2M1), B. longum FGDLZ8M1 was found to most effectively alleviate colitis by reducing the expression of pro-inflammatory cytokines, restoring the colon length, and maintaining the mucosal integrity. The anti-inflammatory mechanisms of B. longum FGDLZ8M1 were related to the inhibition of NF-κB signaling. Genomic analysis indicated that these protective effects of B. longum FGDLZ8M1 may be related to specific genes associated with carbohydrate transport and metabolism and defense mechanisms (e.g., tolerance to bile salts and acids). Correlation analysis indicated that gastrointestinal transit tolerance was the most strongly associated factor. Our findings may contribute to the rapid screening of lactic acid bacterial strains with UC-alleviating effects.

Effects of Bacillus coagulans as an adjunct starter culture on yogurt quality and storage

Bacillus coagulans has been widely studied for its probiotic properties. Therefore, identifying a strain that can be used as an adjunct starter culture for yogurt production would have commercial value. In this study, 30 B. coagulans strains were isolated from vegetable samples from 11 provinces or autonomous regions in China, and their pan-genomic and phylogenetic characteristics were analyzed. Phylogenetic analysis categorized 30 strains into 4 different subphylotypes, including subtype I (11 isolates), subtype II (7 isolates), subtype III (11 isolates), and subtype IV (1 isolate). Four B. coagulans strains (B. coagulans-70, B. coagulans-78, B. coagulans-79, and B. coagulans-100) were randomly selected from each subphylotype of the phylogenetic tree as adjunct starter cultures. Compared with the other tested strains, B. coagulans-70 showed the highest count in yogurt at the end of the manufacturing period. Comparative genome analysis indicated that the different bacterial levels of B. coagulans strains in yogurt may be associated with the abundance of genes related to carbohydrate transport and metabolism (e.g., sucrose utilization). Finally, differences in texture and volatile flavor compound profiles were observed between the yogurt samples. Compared with the other groups, the addition of B. coagulans-70 exerted a positive effect on the appearance and texture of yogurt products. Volatile analysis showed increased quantities of 2-heptanone, 2-nonanone, amyl alcohol, and 2-hydroxy-3-pentanone in the B. coagulans-70 group compared with control yogurts. These results above combined with the results of a sensory evaluation indicated that B. coagulans-70 is the most suitable strain for further use in functional dairy product development.

An appraisal of the gut health modulatory effects of a calf faecal-origin probiotic Lactobacillus salivarius CPN60 using Wistar rats with dextran sulfate sodium-induced colitis

BACKGROUND

Probiotics of varied origins are being developed for augmenting the gut health of human and animals. The present study aimed to evaluate the effect of a calf-origin probiotic supplement on the gut health of Wistar rats for both healthy and colitis conditions.

RESULTS

Forty-eight rats were randomly distributed into four equal groups. The 42-day study involved feeding basal diet alone (CON) or diet supplemented with the calf-origin Lactobacillus salivarius strain CPN60 (PRO). The third (CONc) and fourth (PROc) groups of rats also received the same dietary treatments (CON and PRO, respectively) but were subjected to dextran sulfate sodium (DSS)-induced colitis after 32 days of feeding. The results of a digestion trial conducted after 5 days of DSS administration revealed no influence of probiotic on the digestibility of nutrients. However, the reduced digestibility of protein and fat seen in the CONc rats was improved in the PROc group. The concentrations of lactate and acetate, propionate and butyrate, as well as total short-chain fatty acids (SCFA), were increased (P < 0.05) in the caecal and colonic digesta upon probiotic supplementation, together with significantly reduced colonic ammonia levels. Furthermore, there were reductions (P < 0.05) in acetate, butyrate and total SCFA levels in the caecal contents as a result of colitis. Probiotic supplementation increased (P < 0.05) lactobacilli and bifidobacteria counts in the colon, whereas clostridia and coliform counts were reduced (P < 0.05). These were reversed by the probiotic supplementation.

CONCLUSION

Dietary supplementation of L. salivarius CPN60 had a positive effect with respect to improving the overall gut health of healthy rats, as well as that of rats exposed to experimental colitis. © 2020 Society of Chemical Industry.

Probiotic lactobacilli: Can be a remediating supplement for pandemic COVID-19. A review

In recent years increased attention is focussed on microorganisms inhabiting the digestive system that provides prophylactic and therapeutic benefits to the host. After Metchnikoff exposed the secret behind Bulgarian peasants' extended longevity, a graze to incorporate the responsible microbes in functional food emerged. Then interest towards microbe-rich food went to the vegetative phase for some time, but now a renaissance to engage these wonder microbes in the healthcare sector is increasing. With a new definition, probiotics, these good microbes have been widely applied in different types of products, either as pharmaceuticals, nutritional supplements, or foods. Probiotics, a significant source in functional dairy products, claims diverse roles such as improving intestinal tract health, enhancing the immune system, synthesizing and enhancing the bioavailability of nutrients, reducing symptoms of lactose intolerance, decreasing the prevalence of allergy in susceptible individuals, and reducing the risk of certain cancers. In the recent COVID-19 issue, searches are going fast to use probiotics as vaccine carriers, dysbiosis balancer, and immunity booster. The high expectation from probiotics expanded the development of bioengineered probiotics as new-generation probiotics. From the animal model and in vitro studies, the probiotic intervention is extrapolated to innate and adaptive immunity inducer against SARS viral infections. The possibility of using it as prophylactic and therapeutic agents in COVID-19 is explored. However, its significant activity against corona virus-induced respiratory syndromes is questioned by a few researchers also. The emerging citations on the research approach and meta-analysis of probiotic intervention against the re-emerging pandemic viral attack on the respiratory and gastrointestinal domains need to be analyzed in this context. As it is essential to understand the reality of recent experimental outcomes in the probiotic approach towards SARS-CoV-2 prevention, management, and control, the recent publications were focused on this review.

Functional and Genomic Characterization of Ligilactobacillus salivarius TUCO-L2 Isolated From Lama glama Milk: A Promising Immunobiotic Strain to Combat Infections

Potential probiotic or immunobiotic effects of lactic acid bacteria (LAB) isolated from the milk of the South American camelid llama (Lama glama) have not been reported in published studies. The aim of the present work was to isolate beneficial LAB from llama milk that can be used as potential probiotics active against bacterial pathogens. LAB strains were isolated from llama milk samples. In vitro functional characterization of the strains was performed by evaluating the resistance against gastrointestinal conditions and inhibition of the pathogen growth. Additionally, the adhesive and immunomodulatory properties of the strains were assessed. The functional studies were complemented with a comparative genomic evaluation and in vivo studies in mice. Ligilactobacillus salivarius TUCO-L2 showed enhanced probiotic/immunobiotic potential compared to that of other tested strains. The TUCO-L2 strain was resistant to pH and high bile salt concentrations and demonstrated antimicrobial activity against Gram-negative intestinal pathogens and adhesion to mucins and epithelial cells. L. salivarius TUCO-L2 modulated the innate immune response triggered by Toll-like receptor (TLR)-4 activation in intestinal epithelial cells. This effect involved differential regulation of the expression of inflammatory cytokines and chemokines mediated by the modulation of the negative regulators of the TLR signaling pathway. Moreover, the TUCO-L2 strain enhanced the resistance of mice to Salmonella infection. This is the first report on the isolation and characterization of a potential probiotic/immunobiotic strain from llama milk. The in vitro, in vivo, and in silico investigation performed in this study reveals several research directions that are needed to characterize the TUCO-L2 strain in detail to position this strain as a probiotic or immunobiotic that can be used against infections in humans or animals, including llama.

Lactobacillus salivarius LI01 encapsulated in alginate-pectin microgels ameliorates D-galactosamine-induced acute liver injury in rats

Acute liver failure is a clinical emergency associated with high mortality. Accumulating evidence indicates that gut microbiota participates in the progression of liver injury, and preventive therapies based on altering gut microbiota are of great interest. Previous studies demonstrated that Lactobacillus salivarius LI01 attenuates hepatic injury, though efficiency in curtailed in the harsh environment in the gastrointestinal tract. In this study, a system to encapsulate LI01 in alginate-pectin (AP) microgels was investigated. Encapsulation significantly enhances probiotic viability for long-term storage and heat treatment, and in simulated gastrointestinal fluids (SGF or SIF) and bile salt solutions. Acute liver injury was induced in Sprague-Dawley (SD) rats by D-galactosamine (D-GaIN) injection following pretreatment with probiotics. Liver and gut barrier function, cytokines, liver and gut histology, bacterial translocation, and gut microbiota were assessed. Administration of encapsulated LI01 more effectively upregulates hepatic anti-inflammatory cytokine IL-10 and TLR-3, restores expressions of gut barrier biomarkers Claudin-1 and MUC2 and attenuates destruction of mucosal ultrastructure compared with unencapsulated probiotics pretreatment. Pretreatment with AP-LI01 microgels altered the microbial community, decreasing the abundance of pathogenic taxa Ruminiclostridium, Dorea and Ruminococcaceae_UCG-004 and enriching beneficial taxa Ruminococcaceae_UCG-014, Eubacterium, and Prevotella_1 that produce short-chain fatty acids. These results suggest that AP encapsulation of LI01 boosts viability and attenuates liver injury by reducing inflammation and restoring intestinal barrier function. These beneficial effects are probably due to alternation of gut flora. These findings provide new insight into encapsulation technology and prevention of liver failure. KEY POINTS: • Alginate-pectin encapsulation enhances the viability of Lactobacillus salivarius LI01 under simulated commercial conditions and simulated gastrointestinal environment. • AP-LI01 microgel attenuates hepatic and intestinal inflammation and restores gut barrier function. • AP-LI01 microgel alters gut microbial community with increased SCFAs producers and decreased pathogenic microbes. • Beneficial improvements after administration of probiotics are highly associated with alternation of gut microbial community.

The Role of Gut Microbiota Biomodulators on Mucosal Immunity and Intestinal Inflammation

Alterations of the gut microbiota may cause dysregulated mucosal immune responses leading to the onset of inflammatory bowel diseases (IBD) in genetically susceptible hosts. Restoring immune homeostasis through the normalization of the gut microbiota is now considered a valuable therapeutic approach to treat IBD patients. The customization of microbe-targeted therapies, including antibiotics, prebiotics, live biotherapeutics and faecal microbiota transplantation, is therefore considered to support current therapies in IBD management. In this review, we will discuss recent advancements in the understanding of host−microbe interactions in IBD and the basis to promote homeostatic immune responses through microbe-targeted therapies. By considering gut microbiota dysbiosis as a key feature for the establishment of chronic inflammatory events, in the near future it will be suitable to design new cost-effective, physiologic, and patient-oriented therapeutic strategies for the treatment of IBD that can be applied in a personalized manner.