Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers.

A novel endophytic actinomycete, strain MEP2-6T, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6T is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H6) was the predominant menaquinone, whereas iso-C16:0 and iso-C15:0 were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6T was closely related to Amycolatopsis lexingtonensis NRRL B-24131T (99.4%), A. pretoriensis DSM 44654T (99.3%), and A. eburnea GLM-1T (98.9%). Notably, strain MEP2-6T displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653T (=NRRL B-24131T), A. eburnea GLM-1T, and A. pretoriensis DSM 44654T, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6T could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6T (=JCM 36309T = TBRC 17632T = NBRC 116395T). Amycolatopsis solani MEP2-6T was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6T to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6T is a promising candidate as a novel biocontrol agent and antibiotic producer.

Sporolactobacillus mangiferae sp. nov., a spore-forming lactic acid bacterium isolated from tree bark in Thailand.

A Gram-stain-positive, facultatively anaerobic and endospore-forming rod-shaped bacterium, designed strain CPB3-1T, was isolated from tree bark. This homofermentative strain produced dl-lactic acid from glucose. It grew at 20-45 °C, pH 4.0-9.5 and in 0-3.0 % (w/v) NaCl. It contained meso-diaminopimelic acid in cell-wall peptidoglycan and had menaquinone with seven isoprene units (MK-7) as the predominant component. The major fatty acid was anteiso-C17 : 0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown lipid. Based on the results of 16S rRNA gene sequence analysis, strain CPB3-1T belonged to the genus Sporolactobacillus and was closely related to Sporolactobacillus kofuensis DSM 11701T and Sporolactobacillus spathodeae BK117-1T (both 96.7 % similarity), Sporolactobacillus inulinus NRIC 1133T and Sporolactobacillus terrae DSM 11697T (both 96.6 % similarity), and Sporolactobacillus shoreicorticis MK21-7T, Sporolactobacillus laevolacticus DSM 442T, Sporolactobacillus shoreae BK92T and Sporolactobacillus pectinivorans GD201205T (all 95.8-96.5 % similarity). The draft genome of strain CPB3-1T contained 2 930 919 bps with 3117 coding genes. The DNA G+C content was 45.1 mol%. The digital DNA-DNA hybridization values between strain CPB3-1T and closely related type strains were 19.2-24.0 %. The average nucleotide identity (84.0-87.6 %) and average amino acid identity (66.5-76.3 %) values were lower than the cut-off values for species delineation. Strain CPB3-1T was clearly distinguished from related Sporolactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and the results of draft genome analysis. Therefore, the strain represents a novel species of the genus Sporolactobacillus, for which the name Sporolactobacillus mangiferae sp. nov. is proposed. The type strain is CPB3-1T (=JCM 35082T=TISTR 10004T).

Influence of dietary supplementation with new Lactobacillus strains on hematology, serum biochemistry, nutritional status, digestibility, enzyme activities, and immunity in dogs.

Background and Aim: The use of antibiotics is associated with many side effects, with the development of bacterial resistance being particularly important. It has been found that dogs and their owners host similar resistant bacteria. This contributes to increased concurrent bacterial resistance and a possible trend of increased bacterial resistance in humans. Thus, using probiotics in dogs is an alternative option for preventing and reducing the transmission of bacterial resistance from dogs to humans. Probiotics are characterized by their potential to endure low pH levels and high concentrations of bile acids in the gastrointestinal tract. Lactobacilli are more acid-tolerant and resistant to bile acid, so they are ideal probiotics to be added to the canine diet. According to the previous studies, the benefits of Lactobacillus are a stable nutritional status and greater digestibility, along with improved fecal scores and reduced ammonia in dogs. However, no studies have been conducted with Lactobacillus plantarum CM20-8 (TISTR 2676), Lactobacillus acidophilus Im10 (TISTR 2734), Lactobacillus rhamnosus L12-2 (TISTR 2716), Lactobacillus paracasei KT-5 (TISTR 2688), and Lactobacillus fermentum CM14-8 (TISTR 2720), or their use in combination. Hence, the aim of this study was to examine the possible effects of the aforementioned Lactobacillus on hematological indices, nutritional status, digestibility, enzyme activities, and immunity in dogs. From the results, a new and safe strain of Lactobacillus may emerge for use as a probiotic in the future. Materials and Methods: In this study, 35 dogs were allocated equally into seven groups: Group 1 received a basal diet (control), while Groups 2-7 received the same diet further supplemented with L. plantarum CM20-8 (TISTR 2676), L. acidophilus Im10 (TISTR 2734), L. rhamnosus L12-2 (TISTR 2716), L. paracasei KT-5 (TISTR 2688), L. fermentum CM14-8 (TISTR 2720), or a mixture of probiotics (L. plantarum, L. acidophilus, L. rhamnosus, L. paracasei, and L. fermentum), respectively. All probiotics were administered at a dose of 109 colony-forming unit/dog for 28 days. Nutritional status, hematology, serum biochemistry, digestibility, enzyme activities, and immunity parameters were assessed. Results: There were no differences among the groups in body weight, feed intake, body condition score, fecal score, and fecal dry matter on the different sampling days. The hematology and serum biochemical analyses showed a difference only in creatinine activity (p < 0.001), with higher values in group L. fermentum CM14-8 (TISTR 2720) and lower values in group L. paracasei KT-5 (TISTR 2688) than in controls. However, all measurements were within the normal laboratory reference ranges. Fecal characteristics (fecal ammonia and fecal pH), fecal digestive enzyme activities, serum immunoglobulin (IgG), and fecal IgA did not differ significantly among the groups (p > 0.05). Conclusion: Lactobacillus plantarum CM20-8 (TISTR 2676), L. acidophilus Im10 (TISTR 2734), L. rhamnosus L12-2 (TISTR 2716), L. paracasei KT-5 (TISTR 2688), and L. fermentum CM14-8 (TISTR 2720), along with their mixture are safe and non-pathogenic additives for use as new probiotic strains of Lactobacillus in dogs. Although the new Lactobacillus strains had no effect on hematology, serum biochemistry, nutritional status, digestive enzyme activities, immunity, body weight, feed intake, or body condition scores in dogs, further studies should investigate the intestinal microbiota and the development of clinical treatments.

Safety and Effects of Lactobacillus paracasei TISTR 2593 Supplementation on Improving Cholesterol Metabolism and Atherosclerosis-Related Parameters in Subjects with Hypercholesterolemia: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.

Probiotics have the potential as a multi-target approach to modulate hypercholesterolemia associated with premature atherosclerosis. Various strains of Lactobacillus paracasei have been reported to affect hypercholesterolemia positively. This study aimed to investigate the effects of L. paracasei TISTR 2593 on lipid profile, cholesterol metabolism, and atherosclerosis according to the registration of Thai Clinical Trial Registry as identification number TCTR 20220917002. A total of 50 participants with hypercholesterolemia were randomly and equally assigned to consume L. paracasei TISTR 2593 or a placebo in maltodextrin capsules daily. Biomarkers of lipid profiles, oxidative stress state, inflammatory state, and other biological indicators were examined on days 0, 45, and 90. The results showed that subjects taking the L. paracasei TISTR 2593 could significantly reduce the level of serum low-density lipoprotein-cholesterol (p < 0.05), malondialdehyde (p < 0.001), and tumor necrosis factor-α (p < 0.01). Moreover, L. paracasei TISTR 2593 increased the level of serum apolipoprotein E (p < 0.01) and adiponectin (p < 0.001) significantly. No changes in serum total cholesterol, high-density lipoprotein-cholesterol, triglyceride, total bile acids, and monocyte chemoattractant protein-1 were observed during L. paracasei TISTR 2593 supplementation. Therefore, L. paracasei TISTR 2593 could be an adjuvant probiotic supplement to ameliorate hypercholesterolemia and prevent or delay the development of atherosclerosis.

Bacillus salacetis sp. nov., a slightly halophilic bacterium from Thai shrimp paste (Ka-pi).

A Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4T, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4T grew at pH 6.0-9.0 (optimum, 7.5), at 20-40 °C (37 °C) and in 0-15 % (w/v) NaCl (1-3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C15 : 0 and anteiso-C15 : 0 as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4T belonged to the genus Bacillus and was closely related to Bacillus vietnamensis JCM 11124T, Bacillus marisflavi JCM 11544T, Bacillus aquimaris JCM 11545T and Bacillusoryzaecorticis JCM 19602T, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4T was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4T were 70.0 and 84.3 %, respectively, and the digital DNA-DNA hybridization value was 20 % in comparison with the draft genome of B. vietnamensis JCM 11124T. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus Bacillus and the name Bacillus salacetis sp. nov. is proposed. The type strain is SKP7-4T (=JCM 33205T=KCTC 43014T=TISTR 2596T).

Paenibacillus cathormii sp. nov., isolated from tree bark.

A Gram-stain-positive, facultatively anaerobic, rod-shaped and endospore-forming bacterium, strain BK114-2T isolated from tree bark in Thailand was characterized taxonomically using a polyphasic approach. Analysis based on comparison of 16S rRNA gene sequences indicated that strain BK114-2T was affiliated to the genus Paenibacillus, and was closely related to Paenibacillus timonensis 2301032T (96.7 % 16S rRNA gene sequence similarity), Paenibacillus phoenicis 3PO2SAT (96.6 %) and Paenibacillus barengoltzii SAFN-016T (96.4 %). Strain BK114-2T contained meso-diaminopimelic acid in its cell-wall peptidoglycan. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown phospholipids, five unknown aminophospholipids and six unknown lipids. The only menaquinone detected was MK-7 and the dominant cellular fatty acids were C16 : 0 (22.9 %), anteiso-C15 : 0 (22.6 %), iso-C16 : 0 (19.4 %) and anteiso-C17 : 0 (14.7 %). The DNA G+C content was 52.0 mol%. Based on these results, strain BK114-2T repreesents a novel species of the genus Paenibacillus, for which the name Paenibacillus cathormii sp. nov. is proposed. The type strain is BK114-2T ( = KCTC 33251T = TISTR 2282T).