Evidence of host specificity in Lactobacillus johnsonii genomes and its influence on probiotic potential in poultry

Direct-fed Microbials (DFM) and Poultry Genomics: A Synergistic Approach to Sustainable Antibiotic Free Farming

Improper usage of antibiotics in poultry production is a great threat to the ecosystem because their residues can enter into the food chain or leach into soil or water systems and increase antibiotic resistance risks. Hence, direct-fed microbials (DFMs) have gained recognition as a sustainable and viable alternative to antibiotics in poultry production, capitalizing on the relationship between microbial genetics, host genomics, and gut microbiota. This review delves into the genetic and host genomic mechanisms through DFMs effects including the enhancement of nutrient metabolism, modulation of gut microbiota and strengthening of the host immunity. The revolution of multi-omics has participated in the identification of probiotic strains with desirable traits and revealed their impact on host gene expression, particularly in genes related to intestinal health, such as tight junction proteins and mucins. Furthermore, the review summarizes the benefits of using DFMs in poultry production, the factors affecting their efficacy and their challenges and limitations. Future research integrating host and microbial genomics, along with precision microbiome engineering, holds promise for maximizing the potential of DFMs in advancing sustainable poultry farming practices.

Genomic and transcriptomic insights into vertebrate host-specific Lactobacillus johnsonii adaptation in the gastrointestinal tract

We conducted a comparative genomic analysis of Lactobacillus johnsonii strains isolated from the gastrointestinal tract of diverse vertebrate hosts to explore the genetic basis of host specificity. We then utilized transcriptomics analysis to investigate the expression profile of identified rodent-specific genes in mouse isolate MR1 during in vitro and in vivo growth conditions. There was significant heterogeneity among strains, in both genome sequence and content, with phylogenetic clustering of strains into distinct clades associated with rodent or avian sources. There were not sufficient genomes to identify whether porcine isolates formed their own genetic clade. However, human isolates did not form a distinct clade. Functional enrichment analysis revealed significant enrichment of several genes, including surface proteins and accessory secretory pathway-related genes, as well as tyrosine decarboxylase genes in rodent isolates compared to avian isolates, including in mouse isolate MR1. A total of 40 genes were identified as rodent-associated, and all were transcriptionally active in L. johnsonii MR1. The global transcriptomic analysis of L. johnsonii MR1 was done using cells grown anaerobically, at 37˚C, under both the late-exponential phase and stationary phase, as well as during in vivo growth in the cecum of mono-colonized germ-free mice. Several of these genes were uniquely regulated during late exponential vs stationary phase growth and in vivo colonization in mice, highlighting their potential role in nutrient adaptation and host-microbe interactions.IMPORTANCELactobacillus johnsonii is a well-known probiotic species with health-beneficial properties, including host immunomodulation and pathogen inhibition. Its growing relevance in the medical industry highlights the need to understand its biology, particularly how it adapts to different host environments. In bacteria, niche adaptation is often accompanied by the loss or gain of coding sequences along with changes in the genome size. In this study, we explored the genetic diversity of L. johnsonii strains from the gastrointestinal tracts of various vertebrates such as rodents, birds, swine, and humans. We found associations between genome content and host species of origin and could conceptually demonstrate that these genes are being differentially transcribed under varying conditions. Several functions were associated with specific host groups, suggesting that L. johnsonii strains have adapted to their hosts over time.

Complete Genome Sequence and Probiotic Properties of Pediococcus acidilactici CLP03 Isolated from Healthy Felis catus

Probiotics are available from various sources, including the gastrointestinal tract of healthy animals. In this study, Pediococcus acidilactici was isolated for the first time from Felis catus and evaluated for its functionality. The findings revealed that P. acidilactici CLP03 exhibited inhibitory properties against pathogenic bacteria (E. coli, Salmonella, S. aureus, P. aeruginosa, and L. monocytogenes). Then, survival of strains exposed to pH 2.5, 0.3% bile salts, 0.5% bile salts, and gastrointestinal fluids was 63.97%, 98.84%, 87.95%, and 52.45%, respectively. Also, P. acidilactici CLP03 demonstrated high hydrophobicity (69.63-82.03%) and self-aggregation (73.51-81.44%), negative for hemolytic, and was susceptible to clindamycin. Finally, the scavenging rates of DPPH, ABTS, and O2- were 53.55%, 54.81%, and 85.13%, respectively, which demonstrated that the strain CLP03 has good oxidation resistance. All these characteristics contribute to the survival, colonization, and functionality of the strain in the gastrointestinal tract, indicating their excellent probiotic potential. On the other hand, animal experiments (KM mice, randomly assigned to four groups) showed that the gavage of CLP03 had no toxic effects on mice, increased the serum SOD content, and decreased the MDA and BUN contents, which revealed gavage of CLP03 significantly increased the antioxidant capacity of mice in vivo. In addition, complete genome annotation showed that P. acidilactici CLP03 had 1976 CDS genes, and the numbers of CRISPR, gene islands, and phages were 8, 3, and 6, respectively. In conclusion, P. acidilactici CLP03 could be a candidate functional cat probiotic to enhance animal health and welfare.

Probiotic Potential of Enterococcus lactis GL3 Strain Isolated from Honeybee (Apis mellifera L.) Larvae: Insights into Its Antimicrobial Activity Against Paenibacillus larvae

This study aimed to address the need for effective probiotics and antibacterial agents to combat American foulbrood disease in honeybees, caused by Paenibacillus larvae. In the context of declining honeybee populations due to pathogens, we isolated eight lactic acid bacteria (LAB) strains from honeybee larvae (Apis mellifera L.) and evaluated their probiotic potential and inhibitory effects against P. larvae. Methods included probiotic property assessments, such as acid and bile salt resistance, hydrophobicity, auto-aggregation, co-aggregation with P. larvae, antioxidant capacities, osmotolerance to 50% sucrose, and antibiotic susceptibility. Results indicated that the GL3 strain exhibited superior probiotic attributes and potent inhibitory effects on P. larvae. Whole-genome sequencing revealed GL3 to be an Enterococcus lactis strain with genetic features tailored to the honeybee larval gut environment. Pangenome analysis highlighted genetic diversity among E. lactis strains, while molecular docking analysis identified aborycin, a lasso peptide produced by GL3, as a promising inhibitor of bacterial cell wall synthesis. These findings suggested that GL3 was a promising probiotic candidate and antibacterial agent for honeybee health management, warranting further investigation into its in vivo efficacy and potential applications in beekeeping practices.

Developing Gut-Healthy Strains for Pets: Probiotic Potential and Genomic Insights of Canine-Derived Lactobacillus acidophilus GLA09

Probiotics are widely used to improve pet health and welfare due to their significant biological activity and health benefits. Lactobacillus acidophilus GLA09 was derived from the intestinal tract of healthy beagles. The safety and suitability evaluation of GLA09 was completed through a combination of whole genome sequence and phenotypic analyses, including tests for the inhibition of harmful bacteria, acid resistance, bile salt tolerance, adhesion, and amine-producing substance content. The findings revealed that GLA09 has good gastrointestinal tolerance, inhibits the growth of pathogenic bacteria, and does not produce toxic biogenic amines. The genome of GLA09 comprises one chromosome and one plasmid, with a genome size of 2.10 M and a Guanine + Cytosine content of 38.71%. It encodes a total of 2208 genes, including 10 prophages, and 1 CRISPR sequence. Moreover, 56 carbohydrate-encoding genes were identified in the CAZy database, along with 11 genes for cold and heat stress tolerance, 5 genes for bile salt tolerance, 12 genes for acid tolerance, and 14 predicted antioxidant genes. Furthermore, GLA09 has one lincosamide resistance gene, but there is no risk of transfer. GLA09 harbors a cluster of Helveticin J and Enterolysin A genes linked to antimicrobial activity. Genomic analysis validated the probiotic attributes of GLA09, indicating its potential utility as a significant probiotic in the pet food industry. In summary, L. acidophilus GLA09 has the potential to be used as a probiotic in pet food and can effectively combat intestinal health in pets.

Antimicrobial activity of Lactobacillus casei on Staphylococcus pseudintermedius isolates

BACKGROUND

Antimicrobial resistance is increasing each year. For example, in 2019 it was directly responsible for an estimated >1 million deaths. Additionally, the development of new drugs is much slower, generating enormous concerns about responses to infection in the future health scenario. Therefore, probiotics have emerged as an alternative to antibiotics.

OBJECTIVES

This study aimed to isolate and identify a Lactobacillus casei from healthy canine skin and investigate its antimicrobial effect on isolates of Staphylococcus pseudintermedius originating from dogs with pyoderma.

MATERIALS AND METHODS

L. casei was isolated from skin samples collected with a sterile cotton swab from the inner pinnae of healthy dogs. It was then cultured, identified using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry, and tested against 30 different clinical isolates and one American Type Culture Collection strain of S. pseudintermedius using the spot-on-the-lawn technique. Its safety was assessed through a modified Kirby-Bauer disc diffusion susceptibility test.

RESULTS

L. casei inhibited the growth of all isolates of S. pseudintermedius. The mean value of the inhibition halo of all isolates was 11.3 mm. A significant positive correlation (Pearson's linear correlation = 0.444; p = 0.014) was noted between the inhibitory halos formed by L. casei on the S. pseudintermedius isolates and the halos produced by the tested antimicrobial discs on the same isolates. The L. casei strain demonstrated sensitivity to all tested antimicrobials.

CONCLUSIONS AND CLINICAL RELEVANCE

The study indicates that using commensal bacteria from canine skin, specifically L. casei, to control bacterial infections caused by S. pseudintermedius can be a promising complementary or alternative therapy to antibiotics relevant to animal and human health.

Distinct phenotypes of salivaricin-producing Ligilactobacillus salivarius isolated from the gastrointestinal tract of broiler chickens and laying hens

Ligilactobacillus salivarius harbors bacteriocin genes in its repA-type megaplasmid, specifically salivaricin P (salP), a class IIb bacteriocin. This study aimed to differentiate 25 salP-positive Lig. salivarius strains isolated from the gastrointestinal tract (GIT) of broilers and laying hens. Results showed that 12 isolates were classified as Type A, with active bacteriocins, while the rest were Type B, with no active bacteriocins. In vitro and in silico characterization of salP bacteriocins revealed narrow-spectrum antibacterial activity against Listeria monocytogenes and Enterococcus faecalis. SalP bacteriocins were predicted as positively charged, hydrophobic, small molecular weight (α, 4.097 kDa; ß, 4.285 kDa) bacteriocins with characteristic GXXXG motif. Investigation of the salP gene cluster based on genomic data revealed that Type B strains lacked the lanT and hlyD genes that encode export proteins dedicated to the modification and extracellular transport of mature salP peptides. However, two Type B strains (B4311 and B5258) showed inhibitory activity against L. monocytogenes ATCC19114. Multiplex PCR analysis and synteny mapping analysis revealed that B4311 and B5258 strains harbored the lanT gene, highlighting the importance of LanT protein in the cleavage of leader peptide and excretion of mature peptides. Further analysis revealed that the resistance of Type B strains to salP was attributable to the presence of a dedicated immunity protein, blurring the evolutionary significance of producing active bacteriocins for competitive advantage. Additionally, the loss of export proteins occurred in a polyphyletic manner, consistent with the genetic plasticity of the repA-type megaplasmid. This suggests that the loss of lanT and hlyD is likely in the presence of limited nutritional competitors. In conclusion, the observed differences in salivaricin production of Lig. salivarius exist independent of isolation host and that Type A and Type B strains can coexist in the same environment. Finally, the functional characterization of active salP allows for a better understanding of its potential to control specific bacteria in human food and animal production.

Beneficial effects of duck-derived lactic acid bacteria on growth performance and meat quality through modulation of gut histomorphology and intestinal microflora in Muscovy ducks

Duck-derived lactic acid bacteria (DDL) are a crucial beneficial bacterium in the intestines, contributing significantly to the health of ducks. However, the mechanism by which these DDL improves the growth performance and meat quality of Muscovy duck is not clear. In this study, A total of 800 male Muscovy ducks, initially weighing 50.15 ± 5.37 g, were randomly allocated into 4 groups, each with 4 replicates, consisting of 50 ducks per replicate. The control group consumed deep well water, while the experimental groups were given water supplemented with 1%, 3%, and 5% DDL (1.59×108 CFU/mL). The study duration was 70 d. The results revealed that Muscovy ducks drinks with the DDL significant reduced the feed conversion ratio (FCR) (P < 0.05) and increased the sweetness and richness of duck meat, among which the 5% drinking group has the most significant difference. Further study finding, the DDL significantly increased the height of villi, the ratio of villi height/crypt depth (V/C) on jejunum and colon, and the ratio of acidic mucus, neutral mucus, and glycogen to tissue area in both the duodenum and ileum of Muscovy ducks, and significantly decreased the tunel positive cells. Moreover, DDL significantly enhanced the abundance of genus beneficial bacterium (Bacillus, lentilactobacillus, Bacterodies, Lactobacillus) on duodenum and ileum. Additionally, drink with the DDL elevated the level of IgG in blood and the immune indices of the thymus and the fabricius bursa (P<0.05). Meanwhile, the meat composition analysis demonstrated that Muscovy duck drinks with the DDL raised the level of the saturated fatty acid rate(C12:0), and polyunsaturated fatty acid (C18:2 n-6 and C20:5 n-3,), and the monounsaturated (C18:1 n-7, and C18:1 n-9). Furthermore, correlation analysis finding that the growth performance of Muscovy ducks was positively correlated with the height of villi, the ratio of villi height/crypt depth (V/C), the abundance of genus beneficial bacterium. And the meat quality of Muscovy ducks has positively correlated with genus beneficial bacterium in intestinal, glutamic acid, saturated fatty acid rate and polyunsaturated fatty acid. This finding suggest DDL is an effective strategy to improve the growth performance and meat quality of Muscovy ducks by gut histomorphology and intestinal microflora.

Genomic analysis and functional properties of Lactobacillus johnsonii GJ231 isolated from healthy beagles

Probiotics are one of the management tools to improve the host's healthy microbiota. The positive effects of probiotics on host health are species-specific, so probiotics isolated from host's own gut may be most beneficial. Many of the metabolites (e.g., short-chain fatty acids, bacteriocins, and hydrogen peroxide) produced by Lactobacillus johnsonii have specific inhibitory profiles against invading pathogens. In this study, we isolated L. johnsonii GJ231 from the intestinal tract of healthy female beagles. The genome size of 1.763 M encoded a total of 1,691 predicted genes. Many carbohydrate-active enzymes responsible for carbohydrate degradation and the production of short-chain fatty acids were also predicted. The metabolic profile of short-chain fatty acids in L. johnsonii GJ231 was determined using LC-MS/MS. The bacteriocin-producing gene bacteriocin (lactacin F) in L. johnsonii GJ231 was also predicted. In vitro, experiments demonstrated that GJ231 can thrive in weak acids, 0.3% bile salts, and artificial gastrointestinal fluid models. It was tolerant of to high temperatures up to 70°C, was non- hemolytic, inhibited pathogenic bacteria, and had a high antioxidant capacity. In vivo safety experiments conducted in mice revealed that oral administration of GJ231 not only had no toxic side effect but also increased their antioxidant capacity. In conclusion, combining the above test results, which collectively demonstrate that canine-derived L. johnsonii GJ231 was a non-pathogenic, acid-tolerant and bile-salt-tolerant probiotic strain that inhibits pathogenic bacteria and improves host antioxidant function. This may make it a promising candidate for the development of innovative functional foods for pets.

Impact of Pediococcus acidilactici GLP06 supplementation on gut microbes and metabolites in adult beagles: a comparative analysis

There is growing interest in the potential health benefits of probiotics for both humans and animals. The study aimed to investigate the effects of feeding the canine-derived probiotic Pediococcus acidilactici GLP06 to adult beagles by analysing the microbiome and metabolome. Twenty-four healthy adult beagles were randomly assigned to four groups. The CK group received a standard diet, while the three probiotic groups, the LG group (2 × 108 CFU/day/dog), MG group (2 × 109 CFU/day/dog), and HG group (2 × 1010 CFU/day/dog), received the standard diet supplemented with varying amounts of probiotics. The results show that, compared to the CK group, total antioxidant capacity was significantly increased in the MG and HG groups (p < 0.05), and superoxide dismutase and catalase were significantly increased in the HG group (p < 0.05). Compared to the CK group, malondialdehyde and blood urea nitrogen content were significantly decreased in the MG and HG groups (p < 0.05). Additionally, secretory immunoglobulin A activity was significantly increased in the HG group compared to the CK and LG groups (p < 0.05), and immunoglobulin G activity was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). In addition, compared with the CK group, the abundance of Faecalitalea and Collinsella increased in the LG group, and the relative abundance of Tyzzerella and Parasutterella increased in the MG group. The α diversity and the relative abundances of beneficial bacteria (Faecalibacterium, Lachnospiraceae_NK4A1316, and Ruminococcaceae_UCG-005) were higher in the HG group than in the CK group. Furthermore, acetic acid content was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). Butyric acid, isobutyric acid, and the total SCFA content were significantly increased in the HG group compared to the CK group (p < 0.05). Moreover, metabolome analysis revealed 111 upregulated and 171 downregulated metabolites in the HG group. In conclusion, this study presents evidence that supplementing with P. acidilactici GLP06 can have a positive impact on antioxidant activity, immunoproteins, SCFAs, and gut microbiota in adult beagles. These findings highlight the potential of probiotics as a dietary intervention to enhance gut health and overall wellbeing in companion animals.

Characterization of Probiotic Properties and Whole-Genome Analysis of Lactobacillus johnsonii N5 and N7 Isolated from Swine

In our previous microbiome profiling analysis, Lactobacillus (L.) johnsonii was suggested to contribute to resistance against chronic heat stress-induced diarrhea in weaned piglets. Forty-nine L. johnsonii strains were isolated from these heat stress-resistant piglets, and their probiotic properties were assessed. Strains N5 and N7 exhibited a high survival rate in acidic and bile environments, along with an antagonistic effect against Salmonella. To identify genes potentially involved in these observed probiotic properties, the complete genome sequences of N5 and N7 were determined using a combination of Illumina and nanopore sequencing. The genomes of strains N5 and N7 were found to be highly conserved, with two N5-specific and four N7-specific genes identified. Multiple genes involved in gastrointestinal environment adaptation and probiotic properties, including acidic and bile stress tolerance, anti-inflammation, CAZymes, and utilization and biosynthesis of carbohydrate compounds, were identified in both genomes. Comparative genome analysis of the two genomes and 17 available complete L. johnsonii genomes revealed 101 genes specifically harbored by strains N5 and N7, several of which were implicated in potential probiotic properties. Overall, this study provides novel insights into the genetic basis of niche adaptation and probiotic properties, as well as the genome diversity of L. johnsonii.