16S rRNA Gene Sequence Analysis Research Articles

Huangqi Jianzhong Tang treats chronic atrophic gastritis rats by regulating intestinal flora and conjugated bile acid metabolism.

Huangqi Jianzhong Tang (HQJZ) is effective for treating chronic atrophic gastritis (CAG). The present study was carried out to reveal the mechanism of HQJZ in CAG rats. The metabolism and microbial composition of the cecal contents in CAG rats were analyzed through the integration of an untargeted metabolomic approach using ultra-high-performance liquid chromatography coupled with the quadrupole-time of flight mass spectrometry (UHPLC-QTOF-MS) and 16S rRNA gene sequencing, respectively. Finally, MetOrigin analyses were performed to explore the relationship between differential metabolites and intestinal flora. The results showed that HQJZ could significantly regulate metabolic disorders, especially conjugated acid metabolites. 16S rRNA gene sequencing analysis illustrated that HQJZ decreased the abundance of Acetobacter, Desulfovibrio, Escherichia, and Shigella. MetOrigin metabolite traceability analysis showed that the six bile acids associated with HQJZ efficacy included three bacteria-host cometabolites, which were involved in the primary bile acid biosynthesis pathway. Research presented here confirmed that conjugated bile acid metabolism was key to the treatment of CAG by HQJZ and correlates strongly with Bacteroides acidifaciens and Prevotella copri. These findings provide new insights into the mechanisms to explain the efficacy of HQJZ.

Isolation, Characterization, and Investigation on Potential Multi-trait Plant Growth Promoting Rhizobacteria from Wild Banana (Musa itinerans) Rhizospheric Soil

The undertaken study was conducted to isolate and characterize the plant growth promoting rhizobacteria from the rhizospheric soil of Musa itinerans collected from Zaphumi village, Nagaland, Northeast India. The purified bacterial isolates were screened for plant growth-promoting traits namely phosphate solubilization, IAA production, siderophore production, and ammonia production. Out of the 25 isolates, the three best isolates with maximum growth promoting traits were selected and considered for further study for heavy metal and salinity tolerance. All three isolates were able to produce siderophore, whereas, only isolate EZ30 was able to produce IAA. Phosphate solubilization ability was the highest in EZ27 (272.89±2.46), followed by EZ30 (109.70±5.47) and EZ11(89.12±1.87). The isolates also exhibited variable levels of cadmium (30- 280µg/ml) and salinity resistance (2-14%). Based on 16S-rRNA gene sequence analysis, these bacterial isolates were identified as Kosakonia arachidis, Pseudomonas putida and Pseudomonas monteilii. The highest salinity tolerance was shown by P. putida (14%), whereas K. arachidis (4%) and P. monteilii (4%) exhibited similar level of tolerance. The cadmium tolerance was the highest for P. monteilii (280 µg/ml), followed by K. arachidis (80 µg/ml) and P. putida (30 µg/ml). Inoculation of Cicer arietinum L. with these three isolates significantly enhanced the growth parameter such as shoot and root length (p≤ 0.05), root and shoot fresh weight and dry weight (p≤ 0.05), except for EZ27 and EZ11 where there was no significant difference in shoot dry weight (p≥ 0.05). Overall, the three selected PGPR strains showed potential biofertilizer traits (phosphate solubilizing, IAA producing, siderophore production, salinity, and cadmium tolerant) to be used in the agricultural fields promoting sustainable practices.

Intestinal flora in the constipation patients before versus after lactulose intervention.

This study aimed to investigate the characteristics of intestinal flora in patients with chronic functional constipation before and after lactulose intervention. Twenty-nine patients with constipation in the treatment group received oral lactulose (15 mL/d) for a month. Twenty healthy subjects served as controls. Stool specimens were collected before and after lactulose treatment. Fecal bacteria were examined by 16SrRNA gene sequencing and bioinformatics analysis. After lactulose treatment, most bacteria in the constipation group, including Bifidobacteria, Bacillus cereus, Prevotella, Bacillus, Anaerostipes, Oribacterium, and Mogibacterium increased as compared to those in the healthy control group. Anaerotruncus declined in the healthy control group after lactulose treatment. Our study shows lactulose can increase the abundance of probiotics, optimize the intestinal microenvironment, and alleviate constipation.

Biological functions of endophytic bacteria in Robinia pseudoacacia 'Hongsen'.

Endophytes and their host plants have co-evolved for a very long time. This relationship has led to the general recognition of endophytes as a particular class of microbial resources. R. pseudoacacia 'Hongsen' is drought- and barren-resistant species that can be grown in both the north and south of China, efficiently addresses the ecological issues caused by China's 'southern eucalyptus and northern poplar. Up to date, cultured-dependent studies are available for the R. pseudoacacia nitrogen-fixing and other endophytes. Therefore, the present research studied the R. pseudoacacia 'Hongsen,' microbiome in detail by high-throughput sequencing and culture dependant. This study examined microbial species and functional diversity in Robinia pseudoacacia 'Hongsen' using culture-dependent (isolation) and culture-independent techniques. A total of 210 isolates were isolated from R. pseudoacacia 'Hongsen.' These isolates were clustered into 16 groups by the In Situ PCR (IS-PCR) fingerprinting patterns. 16S rRNA gene sequence analysis of the representative strain of each group revealed that these groups belonged to 16 species of 8 genera, demonstrating the diversity of endophytes in R. pseudoacacia 'Hongsen'. 'Bacillus is the most prevalent genus among all the endophytic bacteria. High-throughput sequencing of endophytic bacteria from R. pseudoacacia 'Hongsen' of the plant and the rhizosphere soil bacteria showed that the bacterial populations of soil near the root, leaf, and rhizosphere differed significantly. The microbial abundance decreased in the endophytes as compared to the rhizosphere. We observed a similar community structure of roots and leaves. With and without root nodules, Mesorhizobium sp. was significantly different in R. pseudoacacia 'Hongsen' plant. It was predicted that R. pseudoacacia 'Hongsen' plant endophytic bacteria would play a significant role in the metabolic process, such as carbohydrate metabolism, amino acid metabolism, membrane transport, and energy metabolism.

Actinomycins from Soil-Inhabiting Streptomyces as Sources of Antibacterial Pigments for Silk Dyeing.

Actinobacteria produce a broad spectrum of bioactive substances that are used in the pharmaceutical, agricultural, and biotechnology industries. This study investigates the production of bioactive substances in Streptomyces, isolated from soil under five tropical plants, focusing on their potential as natural antibacterial dyes for silk fabrics. Out of 194 isolates, 44 produced pigments on broken rice as a solid substrate culture. Eight antibacterial pigmented isolates from under Magnolia baillonii (TBRC 15924, TBRC 15927, TBRC 15931), Magnolia rajaniana (TBRC 15925, TBRC 15926, TBRC 15928, TBRC 15930), and Cinnamomum parthenoxylon (TBRC 15929) were studied in more detail. TBRC 15927 was the only isolate where all the crude extracts inhibited the growth of the test organisms, Staphylococcus epidermidis TISTR 518 and S. aureus DMST 4745. The bioactive compounds present in TBRC 15927 were identified through LC-MS/MS analysis as belonging to the actinomycin group, actinomycin D (or X1), X2, and X0β. Also, the ethyl acetate crude extract exhibited non-toxicity at an IC50 value of 0.029 ± 0.008 µg/mL on the mouse fibroblast L-929 assay. From the 16S rRNA gene sequence analysis, TBRC 15927 had 100% identity with Streptomyces gramineus JR-43T. Raw silk dyed with the positive antimicrobial TBRC 15927 extract (8.35 mg/mL) had significant (>99.99%) antibacterial properties. Streptomyces gramineus TBRC 15927 is the first actinomycin-producing strain reported to grow on broken rice and shows promise for antibacterial silk dyeing.

Functional expression of an antimicrobial peptide, belonging to halocin C8 family, from Natrinema sp. RNS21 in Escherichia coli.

Halocins, the proteinaceous antimicrobial agents produced by haloarchaea, may be used for the preservation of salted foods and the treatment of diseases. For their application and function explanation, it is necessary to produce the active recombinants. In this work, a haloarchaeal strain producing halocin was isolated from the salt-fermented shrimp and identified as Natrinema sp. RNS21 by 16S rRNA gene sequence analysis. From 1 L of RNS21 culture, about 0.32mg of halocin with 96% purity was obtained. Based on the molecular weight, stability and amino acid sequence alignment, the antimicrobial peptide belonged to the halocin C8 (HalC8) family. HalC8 was expressed by fusion with glutathione-S-transferase (GST) in E. coli, followed by affinity purification and enterokinase (EK) cleavage. About 6.2mg of recombinant HalC8 with 95% purity was obtained from 1 L of E. coli culture. MALDI-TOF-MS and RP-HPLC analysis indicated that the molecular weight and folding pattern of purified recombinant HalC8 were the same as those of native HalC8. Recombinant HalC8 showed obvious inhibitory activity against Haloferax volcanii. Contrast to native HalC8, the active recombinant HalC8 could be easily produced in a short time with a high yield.

Simulated gastrointestinal digestion of polylactic acid (PLA) biodegradable microplastics and their interaction with the gut microbiota

The accumulation of microplastics (MPs) in the environment as well as their presence in foods and humans highlight the urgent need for studies on the effects of these particles on humans. Polylactic acid (PLA) is the most widely used bioplastic in the food industry and medical field. Despite its biodegradability, biocompatibility, and “Generally Recognized As Safe” (GRAS) status, recent animal model studies have shown that PLA MPs can alter the intestinal microbiota; however, to date, no studies have been reported on the possible gut and health consequences of its intake by humans. This work simulates the ingestion of a realistic daily amount of PLA MPs and their pass through the gastrointestinal tract by combining the INFOGEST method and the gastrointestinal simgi® model to evaluate possible effects on the human colonic microbiota composition (16S rRNA gene sequencing analysis) and metabolic functionality (lactic acid and short-chain fatty acids (SCFA) production). Although PLA MPs did not clearly alter the microbial community homeostasis, increased Bifidobacterium levels tended to increase in presence of millimetric PLA particles. Furthermore, shifts detected at the functional level suggest an alteration of microbial metabolism, and a possible biotransformation of PLA by the human microbial colonic community. Raman spectroscopy and field emission scanning electron microscopy (FESEM) characterization revealed morphological changes on the PLA MPs after the gastric phase of the digestion, and the adhesion of organic matter as well as a microbial biofilm, with surface biodegradation, after the intestinal and colonic phases. With this evidence and the emerging use of bioplastics, understanding their impact on humans and potential biodegradation through gastrointestinal digestion and the human microbiota merits critical investigation.

Unleashing the Potential of Bacterial Isolates from Apple Tree Rhizosphere for Biocontrol of Monilinia laxa: A Promising Approach for Combatting Brown Rot Disease.

Monilinia laxa, a notorious fungal pathogen responsible for the devastating brown rot disease afflicting apples, wreaks havoc in both orchards and storage facilities, precipitating substantial economic losses. Currently, chemical methods represent the primary means of controlling this pathogen in warehouses. However, this study sought to explore an alternative approach by harnessing the biocontrol potential of bacterial isolates against brown rot in apple trees. A total of 72 bacterial isolates were successfully obtained from the apple tree rhizosphere and subjected to initial screening via co-cultivation with the pathogen. Notably, eight bacterial isolates demonstrated remarkable efficacy, reducing the mycelial growth of the pathogen from 68.75 to 9.25%. These isolates were subsequently characterized based on phenotypic traits, biochemical properties, and 16S rRNA gene amplification. Furthermore, we investigated these isolates' production capacity with respect to two enzymes, namely, protease and chitinase, and evaluated their efficacy in disease control. Through phenotypic, biochemical, and 16S rRNA gene-sequencing analyses, the bacterial isolates were identified as Serratia marcescens, Bacillus cereus, Bacillus sp., Staphylococcus succinus, and Pseudomonas baetica. In dual culture assays incorporating M. laxa, S. marcescens and S. succinus exhibited the most potent degree of mycelial growth inhibition, achieving 68.75 and 9.25% reductions, respectively. All the bacterial isolates displayed significant chitinase and protease activities. Quantitative assessment of chitinase activity revealed the highest levels in strains AP5 and AP13, with values of 1.47 and 1.36 U/mL, respectively. Similarly, AP13 and AP6 exhibited the highest protease activity, with maximal enzyme production levels reaching 1.3 and 1.2 U/mL, respectively. In apple disease control assays, S. marcescens and S. succinus strains exhibited disease severity values of 12.34% and 61.66% (DS), respectively, highlighting their contrasting efficacy in mitigating disease infecting apple fruits. These findings underscore the immense potential of the selected bacterial strains with regard to serving as biocontrol agents for combatting brown rot disease in apple trees, thus paving the way for sustainable and eco-friendly alternatives to chemical interventions.

Microbial-Transferred Metabolites of Black Tea Theaflavins by Human Gut Microbiota and Their Impact on Antioxidant Capacity.

Theaflavins (TFs), the primary bioactive components in black tea, are poorly absorbed in the small intestine. However, the biological activity of TFs does not match their low bioavailability, which suggests that the gut microbiota plays a crucial role in their biotransformation and activities. In this study, we aimed to investigate the biotransferred metabolites of TFs produced by the human gut microbiota and these metabolites' function. We profiled the microbial metabolites of TFs by in vitro anaerobic human gut microbiota fermentation using liquid chromatography tandem mass spectrometry (LC-MS/MS) methods. A total of 17 microbial metabolites were identified, and their corresponding metabolic pathways were proposed. Moreover, full-length 16S rRNA gene sequence analysis revealed that the TFs altered the gut microbiota diversity and increased the relative abundance of specific members of the microbiota involved in the catabolism of the TFs, including Flavonifractor_plautii, Bacteroides_uniformis, Eubacterium_ramulus, etc. Notably, the antioxidant capacity of the TF sample increased after fermentation compared to the initial sample. In conclusion, the results contribute to a more comprehensive understanding of the microbial metabolites and antioxidant capacity of TFs.

Lactobacillus johnsonii N5 from heat stress-resistant pigs improves gut mucosal immunity and barrier in dextran sodium sulfate-induced colitis

Developing effective strategies to prevent diarrhea and associated-gut disorders in mammals has gained great significance. Owing to the many health benefits provided by the commensal microbiota of the intestinal tract, such as against environmental perturbation, we explored the host phenotype-associated microbes and their probiotic potential. Based on the observations that the chronic heat stress-exposed weaned piglets present as heat stress-susceptible (HS-SUS) or heat stress-resistant (HS-RES) individuals, we confirmed the phenotypic difference between the two on growth performance (P < 0.05), diarrhea index (P < 0.001), intestinal heat shock protein 70 (HSP70) regulation (P < 0.01), and inflammatory responses (P < 0.01). By comparing the gut microbiome using 16S rRNA gene sequencing and KEGG functional analysis, we found that Lactobacillus johnsonii exhibited significantly higher relative abundance in the HS-RES piglets than in the HS-SUS ones (P < 0.05). Further experiments using a mouse model for chemical-induced inflammation and intestinal injury demonstrated that oral administration of a representative L. johnsonii N5 (isolated from the HS-RES piglets) ameliorated the clinical and histological signs of colitis while suppressing intestinal pro-inflammatory cytokines TNF-α and IL-6 production (P < 0.05). We found that N5 treatment enhanced tight junction proteins ZO-1 and occludin and cytoprotective HSP70 levels under physiological condition and restored their mucosal expressions in colitis (P < 0.05). In support of the high production of the anti-inflammatory cytokine IL-10, N5 promoted the intestinal Peyer's patches MHCII+ and CD103+ dendritic cell populations (P < 0.05), increased the regulatory T (Treg) cell numbers (P < 0.05), and decreased the Th17 population and its IL-17a production under physiological condition and during colitis (P < 0.01). Our results shed light on understanding the interaction between commensal Lactobacillus and the host health, and provide L. johnsonii N5 as an alternative to antibiotics for preventing diarrhea and intestinal diseases.

Pantoea leporis sp. nov., isolated from the faecal material of a rabbit.

A facultative anaerobic, Gram-stain-negative rod-shaped bacterium, designated RT, was isolated from the faecal material of a rabbit (Sylvilagus floridanus). The strain could not be identified using an MALDI Biotyper sirius CA System. The closest matches based on the Bruker library were members of the genera Citrobacter and Pantoea. However, the score value was in the range of no organism identification possible. Based on pairwise of 16S rRNA gene sequence analysis, the isolate was found to be a member of the family Erwiniaceae. The highest sequence similarities were found to the sequences of Pantoea rodasii LMG 26273T (98.7 %), Leclercia adecarboxylata NBRC 102595T (98.5 %) and Enterobacter huaxiensis 090008T (98.4 %). Phylogenetic and whole genome analysis demonstrated that strain RT represents a novel species within the genus Pantoea. The predominant cellular fatty acids of strain RT were C16 : 0 and products present in summed feature 2 (C12 : 0) aldehyde, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). In silico genome analysis showed the presence of enzymes required for production of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The G+C content determined from the genome was 54.94 mol %. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Pantoea for which the name Pantoea leporis sp. nov. is proposed. The type strain is strain RT (=CCUG 76269T=ATCC TSD-291T).

Effects of Menaquinone-7 on the Bone Health of Growing Rats under Calcium Restriction: New Insights from Microbiome-Metabolomics.

Insufficient calcium intake during growth is a global public health concern. The aim of this study was to investigate the effects of dietary menaquinone-7 (MK-7) on bone accrual in growing Sprague-Dawley rats under calcium restriction. Following 13 weeks of treatment, various bone quality parameters, including microarchitecture, were measured. Fecal and cecal samples were subjected to microbiome (16S rRNA gene sequencing) analyses, while metabolomics analysis of the cecum and humerus samples was analyzed based on UHPLC-Q/TOF-MS. We found that calcium deficiency diminished the richness of the microbiome and disrupted microbiome composition, accompanied by an elevation in the relative abundance of Parasutterella. Furthermore, calcium insufficiency escalated the level of isovaleric acid and modified the metabolic profiles. MK-7 supplementation significantly increased the cortical thickness, cortical bone area, and the calcium content of the femur. Apart from improving bone calcium deposition and diminishing bone resorption, the mechanisms underlying the beneficial effects of MK on bone quality also involve the modulation of the host's metabolic pathways and the composition of gut microbiota. The gut-bone axis holds promise as an efficacious target for ameliorating calcium deficiency in children's bone quality, and MK-7 is a promising dietary supplement from this perspective.

Pseudomonas fluorescens RB5 as a Biocontrol Strain for Controlling Wheat Sheath Blight Caused by Rhizoctonia cerealis

Wheat sheath blight is a soil-borne fungal disease caused by Rhizoctonia cerealis and is a serious threat to wheat worldwide. A microbial fungicide is a promising alternative to a chemical fungicide for wheat disease control. In this study, strain RB5 against R. cerealis was isolated from wheat rhizosphere soil, which was identified as Pseudomonas fluorescens according to physiological, biochemical, and 16S rRNA gene sequence analyses. For improving the antifungal activity of RB5, the response surface methodology (RSM) was used to optimize the culture conditions for strain RB5, and the optimal culture conditions are 8.7 g/L of cassava, 5.2 g/L of soybean meal, pH 6.8, a 218 r/min speed, a 31.5 °C temperature, and 54 h of culture time. The inhibition rate of the culture filtrate obtained under this culture condition was up to 79.06%. The investigation of action mechanism showed strain RB5 could produce protease, chitinase, and siderophore, and its culture filtrate disrupted the mycelial morphology and inhibited the activities of three cell-wall-degrading enzymes of R. cerealis. Furthermore, the pot experiment exhibited that RB5 significantly controlled the wheat sheath blight with an efficacy of 71.22%. The evaluation of toxicological safety on an animal indicated that the culture filtrate was safe on mice. Overall, the culture filtrate of RB5 is a very promising microbial fungicide for the control of wheat sheath blight.

Isolation of bacteria with plant growth-promoting properties from microalgae-bacterial flocs produced in high-rate oxidation ponds

ABSTRACT Exploring plant growth-promoting (PGP) bacterial activity of microbial components aggregated by wastewater treatment can reduce dependence on fossil fuel-derived fertilisers. This study describes the isolation and identification of bacteria from microalgae-bacteria flocs (MaB-flocs) generated in high-rate algal oxidation ponds (HRAOP) of an integrated algal pond system (IAPS) remediating municipal wastewater. Amplified 16S rRNA gene sequence analysis determined the molecular identity of the individual strains. Genetic relatedness to known PGP rhizobacteria in the NCBI GenBank database was by metagenomics. Isolated strains were screened for the production of indoles (measured as indole-3-acetic acid; IAA) and an ability to mineralise NH 4 + , PO 4 3 − , and K + . Of the twelve bacterial strains isolated from HRAOP MaB-flocs, four produced indoles, nine mineralised NH 4 + , seven solubilised P, and one K. Potential of isolated strains for PGP activity according to one-way ANOVA on ranks was: ECCN 7b > ECCN 4b > ECCN 6b > ECCN 3b = ECCN 10b > ECCN 1b = ECCN 5b > ECCN 8b > ECCN 2b > ECCN 12b > ECCN 9b = ECCN 11b. Further study revealed that cell-free filtrate from indole-producing cultures of Aeromonas strain ECCN 4b, Enterobacter strain ECCN 7b, and Arthrobacter strain ECCN 6b promoted mung bean adventitious root formation suggestive of the presence of auxin-like biological activity.

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).

Isolation and characterization of Bacillus velezensis strain B19 for biocontrol of Panax notoginseng root rot

Medicine plants such as Panax notoginseng (Sanqi) frequently experience replant failure owing to the accumulation of soilborne pathogens and autotoxins in continuous cropping soil. Bacillus sp. is a commonly used biocontrol agent to combat soilborne pathogens, but further research is needed to understand its impact on controlling Sanqi root rot and the underlying mechanisms. Here, we isolated and screened a Bacillus strain, B19, from Sanqi rhizosphere soil that exhibited potential for inhibiting Sanqi root rot pathogens. We then tested the strain's effect on the incidence of Sanqi root rot in continuous cropping soil, along with its motility/chemotaxis and biofilm formation ability (i.e., potential for root colonization). We also analyzed the strain's genomic characteristics, including potential secondary metabolite synthesis gene clusters. Our results showed that the strain B19 exhibited high inhibitory activity against fungal pathogens (F. solani and F. oxysporum) and could metabolize saponins as a sole carbon source. The application of B19 to continuous cropping soil significantly reduced the incidence of root rot in Sanqi seedlings. B19 was identified as B. velezensis through morphological characteristics, 16S rRNA and gyrA gene sequence analysis, and genome-level annotation. Notably, B19′s genome encodes many genes associated with functions such as motility/chemotaxis and biofilm formation, as well as 13 biosynthetic gene clusters that could encode secondary metabolites, including surfactin, fengycin, and siderophore. Additionally, B19 demonstrated the capability to produce volatile organic compounds that inhibit pathogenic fungi. The motility/chemotaxis and biofilm-forming ability of B19 were enhanced by saponins. Collectively, these properties could enhance B19′s biocontrol ability, thereby reducing the incidence of root rot.

Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis.

Filamentous actinomycetes, designated SL13 and SL54T, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family Streptomycetaceae. They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H8), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to Streptomyces parmotrematis NBRC 115203T. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with Streptantibioticus cattleyicolor DSM 46488T, Streptomyces ferralitis DSM 41836T and Streptomyces rubrisoli DSM 42083T. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of S. cattleyicolor, S. ferralitis, S. parmotrematis and S. rubrisoli; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA-DNA hybridization values. These metrics confirm that isolates SL13 and SL54T belong to a novel species that is most closely related to S. parmotrematis NBRC 115203T and that these strains together with S. ferralitis DSM 41836T, S. rubrisoli DSM 42083T belong to the genus Streptantibioticus. Consequently, it is proposed that the isolates be recognized as a new Streptantibioticus species, Streptantibioticus silvisoli comb. nov., with isolate SL54T (=DSM 111111T=PCM3044T) as the type strain, and that S. ferralitis, S. parmotrematis and S. rubrisoli be transferred to the genus Streptantibioticus as Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov. Emended descriptions are given for the genus Streptantibioticus, the family Streptomycetaceae and for Streptomyces iconiensis which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that Streptomyces cocklensis be transferred to the genus Actinacidiphila as Actinacidiphila cocklensis comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.

Mariluticola halotolerans gen. nov., sp. nov., a novel member of the family Devosiaceae isolated from South China Sea sediment.

A novel member of class Alphaproteobacteria was isolated from marine sediment of the South China Sea. Cells of strain LMO-2T were Gram-stain negative, greyish in colour, motile, with a single lateral flagellum and short rod in shape with a slight curve. Strain LMO-2T was positive for oxidase and negative for catalase. The bacterium grew aerobically at 10-40 °C (optimum, 25-30 °C), pH 5.5-10.0 (optimum, pH 7.0) and 0-9 % NaCl (w/v; optimum, 2-3 %). Phylogenetic analysis of the 16S rRNA gene sequence and phylogenomic analysis of the whole genome sequence indicated that strain LMO-2T represents a new genus and a new species within the family Devosiaceae, class Alphaproteobacteria, phylum Pseudomonadota. Comparisons of the 16S rRNA gene sequences of strain LMO-2T showed 94.8 % similarity to its closest relative. The genome size is ~3.45 Mbp with a DNA G+C content of 58.17 mol%. The strain possesses potential capability for the degradation of complex organic matter, i.e. fatty acid and benzoate. The predominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1 ω7c 11-methyl. The sole respiratory quinone was ubiquinone-10. The major identified polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phospholipid. Based on the polyphasic taxonomic data, strain LMO-2T represents a novel genus and a novel species for which the name Mariluticola halotolerans gen. nov., sp. nov., was proposed in the family Devosiaceae. The type strain is LMO-2T (=CGMCC 1.19273T=JCM 34934T).

Antibiotic Potential of Marine Actinomycetes of the Genera &lt;i&gt;Streptomyces&lt;/i&gt; and &lt;i&gt;Nocardiopsis&lt;/i&gt;

Due to the emergence of antibiotic resistance in pathogenic microorganisms, it is urgent to search for producers of new antimicrobial metabolites. Actinomycetes are gram-positive mycelial bacteria that produce a large number of antibiotics used in medicine and the agro-industrial complex. Currently, researchers are focused on the search for actinomycetes in ecological niches such as freshwater and marine reservoirs, zones with extreme natural conditions (permafrost soils, glaciers, desert, saline soils, etc.). In this study, cultures of marine actinomycetes were restored after 15 years of storage under vaseline oil. It was shown that all strains retained viability and antibiotic activity at a high level. Based on the results of 16S rRNA gene sequence analysis, the species were identified as: Streptomyces sampsonii 6N, Streptomyces sampsonii 8N, Streptomyces sampsonii 521N, Streptomyces halstedii 22N, Streptomyces brevispora 12N, Streptomyces hirsutus 23N, Streptomyces niveus 14N, Nocardiopsis alba 24N, Nocardiopsis alba 73N, Nocardiopsis alba 85N, Nocardiopsis alba 106N, Nocardiopsis alborubida 722N, Nocardiopsis umidischolae 755N, Nocardiopsis umidischolae 763N. These strains of actinobacteria possessed significant antibiotic activity against the following pathogens: Micrococcus luteus ATCC 9341, Staphylococcus aureus INA 00985, Bacillus subtilis ATCC 6633, Staphylococcus aureus INA 00761 (MRSA — Staphylococcus aureus), Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Pectobacterium carotovorum VKM-B1247, Saccharomyces cerevisiae INA 01042, Candida albicans ATCC 14053, Aspergillus niger ATCC 16404, Aspergillus fumigatus CPB F -37, Fusarium solani VKPM F-890, Fusarium oxysporum VKPM F-148. Therefore, this study evaluated the marine actinomycetes can be potential producers of the novel antibiotics.

Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome.

Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic approach was applied to decipher the impact of the skincare products with pre/postbiotics on skin microbiome and metabolome. Subjects with dry skin applied a body wash and body lotion with or without pre/postbiotics for 6 weeks. Skin hydration was measured at baseline, 3 and 6 weeks. Skin swabs were collected for 16S rRNA gene sequencing, metagenomics and metabolomics analysis. Skin hydration significantly increased in both groups. The prebiotic group significantly reduced opportunistic pathogens, e.g., Pseudomonas stutzeri and Sphingomonas anadarae, and increased the commensals, e.g., Staphylococcus equorum, Streptococcus mitis, Halomonas desiderata. Bacterial sugar degradation pathways were enriched in the prebiotic group, while fatty acid biosynthesis pathways were reduced in control. The changes on skin metabolome profiles by the products were more prominent. The prebiotic group performed greater modulation on many clinically-relevant metabolites compared to control. Correlation analysis showed H. desiderata and S. mitis positively correlated with skin hydration, P. stutzeri and S. anadarae negatively correlated with the metabolites that are positively associated with skin hydration improvement. This holistic study supported a hypothesis that the pre/postbiotics increased skin hydration through the modulation of skin microbiome, metabolic pathways and metabolome.