16S rRNA Gene Sequence Analysis Research Articles

Study on the intervention effect of Epimedium before and after suet-oil-processed on kidney yang deficiency rats based on intestinal flora and fecal metabolomics

Epimedium is a Chinese herbal medicine commonly used in clinical practice to reinforce yang. Previous studies have shown that Epimedium fried with suet oil based has the best effect on warming kidney and promoting yang. Evidence suggests a relationship between kidney yang deficiency syndrome (KYDS) and metabolic disorders of the intestinal microflora. However, the specific interaction between KYDS and the intestinal microbiome, as well as the internal regulatory mechanism of the KYDS intestinal microbiome regulated by Epimedium fried with suet oil, remain unclear. The purpose of this study was to investigate the regulatory effects of different processed products of Epimedium on intestinal microflora and metabolites in rats with kidney yang deficiency, and to reveal the processing mechanism of Epimedium fried with suet oil warming kidney and helping yang. 16S rRNA and LC-MS/MS technology were used to detect fecal samples. Combined with multivariate statistical analysis, differential intestinal flora and metabolites were screened. Then the content of differential bacteria was then quantified using quantitative real-time fluorescence PCR. Furthermore, the correlation between differential bacterial flora and metabolites was analyzed using Spearman's method. The study found that the composition of intestinal flora in rats with kidney yang deficiency changed compared to healthy rats. Epimedium fried with suet oil could increase the levels of beneficial bacteria, while significantly reducing the levels of harmful bacteria. Real-time quantitative PCR results were consistent with 16S rRNA gene sequencing analysis. Fecal metabolomics revealed that KYDS was associated with 30 different metabolites, involving metabolic pathways steroid hormone biosynthesis etc. Moreover, differential bacteria were closely correlated with potential biomarkers. Epimedium could improve metabolic disorders associated with KYDS by acting on the intestinal flora, with Epimedium fried with suet oil demonstrating the most effective regulatory effect. Its potential mechanism may involve the regulation of abnormal metabolism and the impact on the diversity and structure of the intestinal flora.

Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China

Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.

Lactobacillus juensis sp. nov. and Lactobacillus rizhaonensis sp. nov., isolated from the gut of honeybee (Apis mellifera).

Four lactic acid bacteria, designated F690T, F697, F790T and F769-2, were isolated from the gut of honeybee (Apis mellifera). Results of 16S rRNA gene sequence analysis indicated that strains F690T and F697 were phylogenetically related to the type strains of Lactobacillus kimbladii, Lactobacillus laiwuensis, Lactobacillus kullabergensis and Lactobacillus huangpiensis, having 99.1-99.6 % 16S rRNA gene sequence similarities; and that strains F790T and F769-2 were most closely related to the type strain of Lactobacillus melliventris, having 99.2-99.3 % 16S rRNA gene sequence similarities. The phylogenies based on concatenated pheS, rpoA, gyrB, hsp60, recA, rpoB and tuf sequences and based on whole genome sequences were identical to that based on 16S rRNA gene sequences. Strains F690T and F697 exhibited the highest average nucleotide identity (ANI; 92.1-93.2 %), digital DNA-DNA hybridization (dDDH; 50-50.1 %) and average amino acid identity (AAI; 94.9-95.1 %) values with L. kimbladii Hma2NT. Strains F790T and F769-2 had the highest ANI (93.1-94 %), dDDH (54.4 %) and AAI (94.4-94.7 %) values with L. melliventris Hma8NT. Based upon the data obtained in the present study, two novel species, Lactobacillus juensis sp. nov. and Lactobacillus rizhaonensis sp. nov., are proposed and the type strains are F690T (=JCM 36259T=CCTCC AB 2023131T) and F790T (=JCM 36260T=CCTCC AB 2023132T), respectively.

Effect of Fermented Milk Supplemented with Nisin or Plantaricin Q7 on Inflammatory Factors and Gut Microbiota in Mice.

Lactic-acid-bacteria-derived bacteriocins are used as food biological preservatives widely. Little information is available on the impact of bacteriocin intake with food on gut microbiota in vivo. In this study, the effects of fermented milk supplemented with nisin (FM-nisin) or plantaricin Q7 (FM-Q7) from Lactiplantibacillus plantarum Q7 on inflammatory factors and the gut microbiota of mice were investigated. The results showed that FM-nisin or FM-Q7 up-regulated IFN-γ and down-regulated IL-17 and IL-12 in serum significantly. FM-nisin down-regulated TNF-α and IL-10 while FM-Q7 up-regulated them. The results of 16S rRNA gene sequence analysis suggested that the gut microbiome in mice was changed by FM-nisin or FM-Q7. The Firmicutes/Bacteroides ratio was reduced significantly in both groups. It was observed that the volume of Akkermansia_Muciniphila was significantly reduced whereas those of Lachnospiraceae and Ruminococcaceae were increased. The total number of short-chain fatty acids (SCFAs) in the mouse feces of the FM-nisin group and FM-Q7 group was increased. The content of acetic acid was increased while the butyric acid content was decreased significantly. These findings indicated that FM-nisin or FM-Q7 could stimulate the inflammation response and alter gut microbiota and metabolic components in mice. Further in-depth study is needed to determine the impact of FM-nisin or FM-Q7 on the host's health.

Polycladomyces zharkentensis sp. nov., a novel thermophilic cellulose- and starch-degrading member of the Bacillota from a geothermal aquifer in Kazakhstan.

A thermophilic, aerobic and heterotrophic filamentous bacterium, designated strain ZKZ2T, was isolated from a pipeline producing hydrothermal water originating from a >2.3 km deep subsurface geothermal source in Zharkent, Almaty region, Kazakhstan. The isolate was Gram-stain-positive, non-motile, heat-resistant and capable of producing a variety of extracellular hydrolases. Growth occurred at temperatures between 55 and 75 °C, with an optimum around 70 °C, and at pH values between 5.5 and 9.0, with an optimum at pH 7.0-7.5 with the formation of aerial mycelia; endospores were produced along the aerial mycelium. The isolate was able to utilize the following substrates for growth: glycerol, l-arabinose, ribose, d-xylose, d-glucose, d-fructose, d-mannose, rhamnose, d-mannitol, methyl-d-glucopyranoside, aesculin, salicin, cellobiose, maltose, melibiose, sucrose, trehalose, melezitose, raffinose, starch, turanose and 5-keto-gluconate. Furthermore, it was able to hydrolyse carboxymethylcellulose, starch, skimmed milk, Tween 60 and Tween 80. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. Our 16S rRNA gene sequence analysis placed ZKZ2T within the genus Polycladomyces, family Thermoactinomycetaceae, with the highest similarity to the type species Polycladomyces abyssicola JIR-001T (99.18 % sequence identity). Our draft genome sequence analysis revealed a genome size of 3.3 Mbp with a G+C value of 52.5 mol%. The orthologous average nucleotide identity value as compared to that of its closest relative, P. abyssicola JIR-001T, was 90.23 %, with an in silico DNA-DNA hybridization value of 40.7 %, indicating that ZKZ2T represents a separate genome species. Based on the phenotypic and genome sequence differences from the other two Polycladomyces species, we propose that strain ZKZ2T represents a novel species, for which we propose the name Polycladomyces zharkentensis sp. nov. The type strain is ZKZ2T (=CECT 30708T=KCTC 43421T).

Impact of vaginal microecological differences on pregnancy outcomes and endometrial microbiota in frozen embryo transfer cycles.

This prospective study investigates the correlation between vaginal microecology and pregnancy outcomes and explores their impact on endometrial microbiota composition during frozen embryo transfer (FET) cycles. Additionally, the impact of transvaginal Lactobacillus supplementation on reproductive outcomes in patients with previous failed cycles was assessed. A total of 379 patients undergoing FET at a reproductive medicine center were categorized into clinical pregnancy (CP), miscarriage (MISC), and non-pregnant (NP) groups. Vaginal specimens were collected for microecological evaluation prior to embryo transfer. Endometrial microbiota samples were obtained during embryo transfer for 16S rRNA gene sequencing analysis to assess endometrial microbiota composition. Vaginal microecological indicators, including pH, Lactobacillus dominance, and leukocyte esterase activity, were measured. Transvaginal Lactobacillus supplementation was investigated in 60 patients with previous failed cycles. Vaginal microecology significantly correlated with pregnancy outcomes, with normal microecology associated with a higher clinical pregnancy rate. Vaginal pH and leukocyte esterase activity were significantly associated with clinical pregnancy. Furthermore, vaginal microecological differences significantly impacted endometrial microbiota composition. However, no significant differences were observed in endometrial microbiota composition among the CP, MISC, and NP groups. Notably, transvaginal Lactobacillus supplementation increased the clinical pregnancy rate without affecting the miscarriage rate. This study highlights that normal vaginal microecology, characterized by lower pH and leukocyte esterase negativity, is associated with a higher likelihood of clinical pregnancy following FET. Importantly, vaginal microecological differences influence endometrial microbiota composition. Moreover, transvaginal Lactobacillus supplementation appears promising in improving clinical pregnancy rates in patients with previous failed cycles. These findings contribute to a better understanding of the interplay between vaginal and endometrial microbiota and offer potential interventions to enhance reproductive success in assisted reproductive technologies.

Electroacupuncture at ST25 corrected gut microbial dysbiosis and SNpc lipid peroxidation in Parkinson's disease rats.

Parkinson's disease (PD) remains one kind of a complex, progressive neurodegenerative disease. Levodopa and dopamine agonists as widely utilized PD therapeutics have not shown significant positive long-term outcomes. Emerging evidences indicate that electroacupuncture (EA) have potential effects on the therapy of nervous system disorders, particularly PD, but its specific underlying mechanism(s) remains poorly understood, leading to the great challenge of clinical application and management. Previous study has shown that acupuncture ameliorates PD motor symptoms and dopaminergic neuron damage by modulating intestinal dysbiosis, but its intermediate pathway has not been sufficiently investigated. A rat model of PD was induced using rotenone. The therapeutic effect of EA on PD was assessed using the pole and rotarod tests and immunohistostaining for tyrosine hydroxylase (TH) in the substantia nigra (SN) of brain. The role of gut microbiota was explored using 16S rRNA gene sequencing and metabonomic analysis. PICRUSt2 analysis, lipidomic analysis, LPS and inflammatory factor assays were used for subsequent exploration and validation. Correlation analysis was used to identify the key bacteria that EA regulates lipid metabolism to improve PD. The present study firstly reappeared the effects of EA on protecting motor function and dopaminergic neurons and modulation of gut microbial dysbiosis in rotenone-induced PD rat model. EA improved motor dysfunction (via the pole and rotarod tests) and protected TH+ neurons in PD rats. EA increased the abundance of beneficial bacteria such as Lactobacillus, Dubosiella and Bifidobacterium and decreased the abundance of Escherichia-Shigella and Morganella belonging to Pseudomonadota, suggesting that the modulation of gut microbiota by EA improving the symptoms of PD motility via alleviating LPS-induced inflammatory response and oxidative stress, which was also validated by various aspects such as microbial gene functional analysis, fecal metabolomics analysis, LPS and inflammatory factor assays and SNpc lipidomics analysis. Moreover, correlation analyses also verified strong correlations of Escherichia-Shigella and Morganella with motor symptoms and SNpc lipid peroxidation, explicating targets and intermediate pathways through which EA improve PD exercise symptom. Our results indicate that the improvement of motor function in PD model by EA may be mediated in part by restoring the gut microbiota, which intermediate processes involve circulating endotoxins and inflammatory mediators, SNpc oxidative stress and lipid peroxidation. The gut-microbiome - brain axis may be a potential mechanism of EA treatment for the PD.

Alleviation of allergic asthma by rosmarinic acid via gut-lung axis

BackgroundAsthma affects 3% of the global population, leading to over 0.25 million deaths. Due to its complexity, asthma is difficult to cure or prevent, and current therapies have limitations. This has led to a growing demand for alternative asthma treatments. We found rosmarinic acid (RosA) as a potential new drug candidate from natural medicine. However, RosA has poor bioavailability and remains mainly in the gastrointestinal tract after oral administration, suggesting the involvement of gut microbiota in its bioactivity. PurposeTo investigate the mechanism of RosA in alleviating allergic asthma by gut-lung axis. MethodsWe used 16S rRNA gene sequencing and metabolites analysis to investigate RosA's modulation of gut microbiota. Techniques of molecular biology and metabolomics were employed to study the pharmacological mechanism of RosA. Cohousing was used to confirm the involvement of gut microbiota in RosA-induced improvement of allergic asthma. ResultsRosA decreased cholate levels from spore-forming bacteria, leading to reduced 5-hydroxytryptamine (5-HT) synthesis, bronchoconstriction, vasodilation, and inflammatory cell infiltration. It also increased short-chain fatty acids (SCFAs) levels, facilitating the expression of intestinal tight junction proteins to promote intestinal integrity. SCFAs upregulated intestinal monocarboxylate transporters (MCTs), thereby improving their systemic delivery to reduce Th2/ILC2 mediated inflammatory response and suppress eosinophil influx and mucus production in lung. Additionally, RosA inhibited lipopolysaccharide (LPS) production and translocation, leading to reduced TLR4-NFκB mediated pulmonary inflammation and oxidative stress. ConclusionsThe anti-asthmatic mechanism of oral RosA is primarily driven by modulation of gut microbiota-derived 5-HT, SCFAs, and LPS, achieving a combined synergistic effect. RosA is a safe, effective, and reliable drug candidate that could potentially replace glucocorticoids for asthma treatment.

Nesterenkonia marinintestina sp. nov., isolated from the fish intestine.

A Gram-positive, aerobic, non-motile, irregular short rod, nonspore-forming actinobacterial strain, designated GX14115T, was isolated from fish intestine in Beihai City, Guangxi, China and subjected to a taxonomic polyphasic investigation. Colonies were yellow‒green, circular, smooth, central bulge, convex, opaque and 2.0-3.0mm in diameter after growth on 2216E medium at 30°C for 72h. Growth occurred at 4-45°C (optimum 30°C), at pH 4.5-10.0 (optimum pH 7.5) and in the presence of 0-12% NaCl (w/v) (optimum 3.5%). Chemotaxonomic analysis showed that the main menaquinone of strain GX14115T was MK-7. The major cellular fatty acids were anteiso-C15:0 (44.8%), anteiso-C17:0 (20.5%), and iso-C15:0 (16%). The whole-cell sugars were galactose and xylose. The peptidoglycan type was L-Lys-Gly-D-Asp, and the polar lipids were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), one unknown phospholipid (UP), and one unknown glycolipid (UG). The DNA G + C content of the type of strain was 69.5mol%. The 16S rRNA gene sequence analysis revealed that strain GX14115T is affiliated with the genus Nesterenkonia and is closely related to Nesterenkonia sandarakina YIM 70009T (96.5%) and Nesterenkonia lutea YIM 70081T (96.8%). The calculated results indicated that the average nucleotide identity (ANI) values of GX14115T were 74.49-74.78%, to the two aforementioned type strains, and the digital DNA-DNA hybridization (dDDH) values were 20.1-20.7%. Strain GX14115T was proposed as a novel species of the genus Nesterenkonia by the physiological, chemotaxonomic, and phylogenetic data, for whose the name is Nesterenkonia marinintestina sp. nov. The type of strain is GX14115T (= MCCC 1K06658T = KCTC 49495T).

Combined exposure with microplastics increases the toxic effects of PFOS and its alternative F-53B in adult zebrafish

Microplastics (MPs) can adsorb and desorb organic pollutants, which may alter their biotoxicities. Although the toxicity of perfluorooctane sulfonate (PFOS) and its alternative 6:2 chlorinated polyfluorinated ether sulfonate (F-53B) to organisms has been reported, the comparative study of their combined toxic effects with MPs on aquatic organisms is limited. In this study, adult female zebrafish were exposed to 10 μg/L PFOS/F-53B and 50 μg/L MPs alone or in combination for 14 days to investigate their single and combined toxicities. The results showed that the presence of MPs reduced the concentration of freely dissolved PFOS and F-53B in the exposure solution but did not affect their bioaccumulation in the zebrafish liver and gut. The combined exposure to PFOS and MPs had the greatest impact on liver oxidative stress, immunoinflammatory, and energy metabolism disorders. 16S rRNA gene sequencing analysis revealed that the combined exposure to F-53B and MPs had the greatest impact on gut microbiota. Functional enrichment analysis predicted that the alternations in the gut microbiome could interfere with signaling pathways related to immune and energy metabolic processes. Moreover, significant correlations were observed between changes in gut microbiota and immune and energy metabolism indicators, highlighting the role of gut microbiota in host health. Together, our findings demonstrate that combined exposure to PFOS/F-53B and MPs exacerbates liver immunotoxicity and disturbances in energy metabolism in adult zebrafish compared to single exposure, potentially through dysregulation of gut microbiota.

Molecular characterization of antibiotic-resistant bacteria associated with maggots obtained from chicken droppings

BackgroundThe use of maggots, developed from chicken droppings as alternative fish meal might serve as a reservoir and vehicle for the widespread of single and multiple antibiotic resistant bacteria (MARB). This study aimed at investigating antibiotic resistant bacteria from chicken droppings and maggots developed from them, and the associated resistance genes and mobile genetic elements in their genomes. Freshly collected poultry droppings obtained from three commercial poultry farms, in Akure, Nigeria and maggots developed from their composting were plated on Luria–Bertani (LB) agar plates that had been incorporated with antibiotics. The emerged MARB were presumptively identified by conventional cultural microbiological methods and then authenticated using 16S rRNA gene sequence analysis. The antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the genome of MARB were detected by standard molecular tools.ResultsPotential bacterial pathogens isolated include Escherichia coli, Bacillus cereus, Salmonella enterica, Providencia stuartii, P. rettgeri, Pseudomonas aeruginosa, Staphylococcus aureus, Alcaligenes faecalis, Paelnalcaligenes hominis and Micrococcus luteus. Seventeen ARGs were widely distributed among the 19 ARB/MARB. Tetracycline resistance gene was widely distributed among the ARB/MARB with prevalence of 62%, while macrolides and beta lactam resistance gene had 17% and 13%, respectively. At least six MARB isolates showed the presence of two or more class 1 integron, while five isolates was detected to carry two or more class 2 integron among the 19 MARB.ConclusionsThe results highlight a much higher risk of ARGs spreading through maggots derived from chicken droppings to humans and environmental microbiota.

Genomic and phylogenomic analysis of Fusobacteriaceae family and proposal to reclassify Fusobacterium naviforme Jungano 1909 into a novel genus as Zandiella naviformis gen. nov., comb. nov. and reclassification of Fusobacterium necrophorum subsp. funduliforme as later heterotypic synonym of Fusobacterium necrophorum subsp. necrophorum and Fusobacterium equinum as later heterotypic synonym of Fusobacterium gonidiaformans.

The family Fusobacteriaceae is a large family within the phylum Fusobacteriota. The reclassification of F. naviforme as Zandiella naviformis gen. nov., comb. nov. is proposed because of the separate and distinct phylogenetic situation on the basis of the results of 16S rRNA gene sequence analysis, the genetic and genomic differences from all other species and subspecies in the Fusobacteriaceae family. The type strain is ATCC 25832; CCUG 50052; NCTC 13121. In phylogenetic trees drawn using complete genome sequences and 16S rRNA gene sequences, F. necrophorum subsp. funduliforme and F. equinum were clades together with F. necrophorum subsp. necrophorum and F. gonidiaformans, respectively. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between themes exceeded the cut-off values for species delineation. Based on these results, F. necrophorum subsp. funduliforme and F. equinum should be reclassified as later heterotypic synonyms of F. necrophorum subsp. necrophorum and F. gonidiaformans, respectively.

Gut microbiota was highly related to the immune status in chronic obstructive pulmonary disease patients.

This study aimed to explore the profile of gut microbiota and immunological state in COPD patients. 80 fecal and blood samples were collected from 40 COPD patients and 40 healthy controls (HC) and analyzed with 16s-rRNA gene sequencing and immunofactor omics analysis to investigate the profile of gut microbiota and immunologic factors (IFs). The linear discriminant analysis (LDA) effect size (LefSe) was used to determine the biomarker's taxa. The random forest and LASSO regression analysis were executed to screen IFs and develop an IFscore model. The correlation between gut microbiota and IFs, along with the IFscore and the diversity of gut microbiota, was evaluated with the Spearman analysis. The α and β diversity showed that the composition and distribution of gut microbiota in the COPD group differed from that of the HC group. 7 differential taxa at the phylum level and 17 differential taxa at the genus level were found. LefSe analysis screened out 5 biomarker's taxa. 32 differential IFs (up-regulated 27 IFs and down-regulated 5 IFs) were identified between two groups, and 5 IFs (CCL3, CXCL9, CCL7, IL2, IL4) were used to construct an IFscore model. The Spearman analysis revealed that 29 IFs were highly related to 5 biomarker's taxa and enriched in 16 pathways. Furthermore, the relationship between the IFscore and gut microbiota diversity was very close. The gut microbiota and IFs profile in COPD patients differed from that in healthy individuals. Gut microbiota was highly related to the immune status in COPD patients.

Biodiversity of hydrolytic enzymes-producing soil bacteria from a Durian Park, Jombang, Indonesia: Beneficial prospect for sustainable agriculture

Abstract. Ni’matuzahroh, Affandi M, Supriyanto A, Rustantina B, Jaiyah LA, Rahmawati A, Nurhayati H, Sari SK, Khiftiyah AM, Huri D. 2024. Biodiversity of hydrolytic enzymes-producing soil bacteria from a Durian Park, Jombang, Indonesia: Beneficial prospect for sustainable agriculture. Biodiversitas 25: 392-403. Biofertilizer is an alternative to chemical fertilizer that can enhance plant growth but is specific to certain plants and soils. Various biofertilizers have been produced, but the specific biofertilizers to enhance durian growth have not been widely available. This study aims to determine the potential of hydrolytic enzyme-producing bacteria, one of the microbial components of biofertilizers, in the De Durian Park (DDP) area, Wonosalam, Jombang District, Indonesia. The bacteria were isolated using the selective medium plating technique. The obtained isolates were screened for their ability to produce cellulase, amylase, protease, and lipase. The clear zone around the colony indicated the ability of the isolates to produce hydrolytic enzymes, and then the clear zone index was obtained. The best three isolates for each enzyme production were characterized macroscopically, microscopically, and biochemically, then identified using 16S rRNA gene sequence analysis. Fifty-two isolates were successfully obtained from the soil of DDP. The best three cellulolytic bacteria had indices ranging from 1.83 to 2.14, categorized as moderate-strong, identified as Bacillus anthracis, B. pacificus, and B. cereus. The amylolytic bacteria ranged from 1.25 to 1.35, categorized as moderate, and identified as Bacillus anthracis, B. paranthracis, and B. paramycoides. The proteolytic bacteria ranged from 1.33 to 1.50, categorized as moderate, identified as B. pumilus, B. paramycoides, and B. cereus. The lipolytic bacteria ranged from 1.94 to 3.87, categorized as moderate-strong, and were identified as Enterobacter sichuanensis, B. pacificus, and E. asburiae. These cellulolytic, amylolytic, proteolytic, and lipolytic bacteria have the potency as candidates for a biofertilizer formula.

Isolation and identification of Bifidobacterium species from human breast milk and infant feces in Indonesia

Abstract. Dosan R, Mudana SO, Julyanto CMP, Purnama ET, Sugata M, Jo J, Tan TJ. 2024. Isolation and identification of Bifidobacterium species from human breast milk and infant feces in Indonesia. Biodiversitas 25: 337-343. There has been a growing interest in identifying emerging probiotic strains because of their benefits for human health. Many bifidobacteria originated from humans have been reported to possess probiotics properties. They are commonly found in the intestine of breast-fed infants. Hence, this study aimed to isolate and identify bifidobacteria from human breast milk and infant fecal samples in Indonesia and evaluate their probiotic properties. Twenty colonies were isolated from two independent fecal samples and two independent breast milk samples. Ten isolates (BR1-M1, BR1-B1, BR2-5, BR2-6, BR2-12, BS2-PB3, BS2-PB5, BS2-PS1, BS2-PS2, BS2-MB1) showed a compatible phenotypic character with Bifidobacteria based on the Bergey’s Manual, including Gram-positive, irregular rods, no catalase activity, non-spore-forming, and non-motile. Subsequently, four isolates with similar carbohydrate fermentation patterns as Bifidobacterium spp. were selected for further molecular identification based on 16S rRNA gene sequencing analysis. The results showed that BR2-5 and BR2-6 were found to be closely related to Bifidobacterium animalis subspecies lactis with 100 and 98.39% similarity, respectively. Meanwhile, BS2-PS1 and BS2-PB3 were found to be closely related to Bifidobacterium breve with 100 and 98.26% similarity, respectively. Further investigation revealed that BR2-5 and BS2-PB3 were resistant to low pH (?4) and could tolerate the exposure of bile salts (1%). Both isolates survived under different oxidative stress conditions (aerobic and microaerophilic). In conclusion, BR2-5 and BS2-PB3 exhibited promising characteristics as probiotic candidates, though further investigations are required to substantiate these current findings.

Glycomyces niveus sp. nov., a novel actinomycete isolated from sandy soil.

A novel mycelium-forming actinomycete, designated strain NEAU-S30T, was isolated from the sandy soil of a sea beach in Shouguang city, Shandong province, PR China. The strain developed long chains of non-motile cylindrical spores with smooth surfaces on aerial mycelia. The results of a polyphasic taxonomic study indicated that NEAU-S30T represented a member of the genus Glycomyces. The results of 16S rRNA gene sequence analysis indicated that NEAU-S30T was closely related to 'Glycomycesluteolus' (98.97 % sequence similarity), Glycomycesalgeriensis (98.90 %), 'Glycomyces tritici' (98.83 %) and Glycomyces lechevalierae (98.76 %). The average nucleotide identity (ANI) values between NEAU-S30T and 'G. luteolus' NEAU-A15, G. algeriensis DSM 44727T, 'G. tritici' NEAU-C2 and G. lechevalierae DSM 44724T were 87.77, 87.53, 87.41 and 87.80 %, respectively. The digital DNA G+C content of the genomic DNA was 70.5 %. The whole-cell sugars contained ribose and xylose. The predominant menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). The predominant fatty acids were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified glycolipid. On the basis of the results of comparative analysis of genotypic, phenotypic and chemotaxonomic data, the novel actinomycete strain NEAU-S30T (=JCM 33975T=CGMCC 4.7890T) represents the type strain of a novel species within the genus Glycomyces, for which the name Glycomyces niveus sp. nov. is proposed.

487 - Adult atopic dermatitis is associated with impaired oral health and oral dysbiosis - a case-control study

Abstract Background Previous studies linked chronic oral diseases to skin disorders such as psoriasis. However, data about oral health and oral microbiota in atopic dermatitis (AD) is sparse. Objectives To compare the oral health status and oral microbiota of AD patients and healthy controls. Methods This was a prospective sex and age- matched case-control study comparing adult participants with and without dermatologist-verified AD. Exclusion criteria included recent use of oral, topical, or systemic medication that could affect oral health or microbiome assessment. Oral health indices including Gingival Index, Plaque Index, Oral Hygiene Index, Caries Severity Index and prosthodontics status, were assessed by a dentist. Samples of oral flora were collected and subjected to high-throughput 16S rRNA gene sequencing analysis for microbiome analysis. Results Forty-five AD participants and 41 non-AD controls were recruited. The two groups had no significant differences in terms of their demographic and clinical characteristics, except for the higher rate of atopic co-morbidities in the AD group (p&amp;lt;.001). Compared to the control group, participants with AD had significantly poorer plaque (p=0.04) and oral hygiene indices (p=0.04) and a trend towards higher gingival index (p=0.05). The results of the Faith phylogenetic diversity (FDR) test indicated that the oral microbial diversity in the AD group was significantly higher (α-diversity, FDR-adjusted p=0.0007) when compared with the control group. Characterization of the similarities and differences in the composition of the microbial communities between the samples (β-diversity) from the AD patients and controls indicated that they clustered separately. The groups showed significant dissimilarity and distinct clustering of microbial abundance (FDR-adjusted p=0.001). Importantly, higher community diversity was previously linked to periodontitis and gingival disease. Furthermore, AD patients had a significantly increased abundance of taxa correlated with oral diseases and decreased abundance of oral health-associated bacteria. Conclusion AD appears to be associated with poorer oral health and oral dysbiosis, and thus, there is a need to increase the awareness of both patients and physicians about oral health.

Myceligenerans pegani sp. nov., an endophytic actinomycete isolated from Peganum harmala L. in Xinjiang, PR China.

An endophytic actinomycete designated TRM65318T, was isolated from the root of Peganum harmala L. Its taxonomic status was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis indicated that strain TRM65318T is phylogenetically most closely related to Myceligenerans salitolerans XHU 5031T (98.15 %) and Myceligenerans xiligouense DSM 15700T (97.78 %). The peptidoglycan belonged to type A4α. The polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, two unknown lipids and three glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6) and the whole-cell sugars contained glucose, mannose and galactose. Major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Strain TRM65318T had a genome size of 5881012 bp with a genome G+C content of 71.79 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain TRM65318T and the most closely related species were much lower than the thresholds commonly used to define species. At the same time, differences in phenotypic and genotypic data showed that strain TRM65318T could be clearly distinguished from M. salitolerans XHU 5031T. Therefore, it is concluded that strain TRM65318T represents a novel species of the genus of Myceligenerans. The proposed name for this organism is Myceligenerans pegani sp. nov., with type strain TRM65318T (=CCTCC AA 2019057T=LMG 31679T).

Promotion of anaerobic biodegradation of azo dye RR2 by different biowaste-derived biochars: Characteristics and mechanism study by machine learning

The addition of biochar resulted in a 31.5 % to 44.6 % increase in decolorization efficiency and favorable decolorization stability. Biochar promoted extracellular polymeric substances (EPS) secretion, especially humic-like and fulvic-like substances. Additionally, biochar enhanced the electron transfer capacity of anaerobic sludge and facilitated surface attachment of microbial cells. 16S rRNA gene sequencing analysis indicated that biochar reduced microbial species diversity, enriching fermentative bacteria such as Trichococcus. Finally, a machine learning model was employed to establish a predictive model for biochar characteristics and decolorization efficiency. Biochar electrical conductivity, H/C ratio, and O/C ratio had the most significant impact on RR2 anaerobic decolorization efficiency. According to the results, the possible mechanism of RR2 anaerobic decolorization enhanced by different types of biochar was proposed.

Description of Chryseobacterium fluminis sp. nov., a keratinolytic bacterium isolated from a freshwater river.

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated MMS21-Ot14T, was isolated from a freshwater river, and shown to represent a novel species of the genus Chryseobacterium on the basis of the results from a polyphasic approach. The 16S rRNA gene sequence analysis revealed that MMS21-Ot14T represented a member of the genus Chryseobacterium of the family Weeksellaceae and was closely related to Chryseobacterium hagamense RHA2-9T (97.52 % sequence similarity), Chryseobacterium gwangjuense THG A18T (97.46 %) and Chryseobacterium gregarium P 461/12T (97.27 %). The optimal growth of MMS21-Ot14T occurred at 25-30 °C, pH 6.0-7.0 and in the absence of NaCl. MMS21-Ot14T was capable of hydrolysing casein, starch, DNA, Tween 20 and tyrosine. The strain also showed keratinolytic activity with keratin azure and decolourising activity with remazol brilliant blue R (RBBR), which indicated potential ability to degrade keratin and lignin. The main polar lipids of MMS21-Ot14T were phosphatidylethanolamine, unidentified aminophospholipids, unidentified aminolipids, an unidentified phospholipid and several unidentified lipids. The predominant fatty acids of MMS21-Ot14T were iso-C15 : 0 and iso-C17 : 0 3-OH, and the major isoprenoid quinone was menaquinone 6 (MK-6). The whole genome of MMS21-Ot14T was 5 062 016 bp in length with a DNA G+C content of 37.7 %. The average nucleotide identity and digital DNA-DNA hybridisation values between MMS21-Ot14T and phylogenetically related members of the genus Chryseobacterium were well below the threshold values for species delineation. It is evident from the results of this study that MMS21-Ot14T should be classified as representing a novel species of the genus Chryseobacterium, for which the name Chryseobacterium fluminis sp. nov. (type strain, MMS21-Ot14T = KCTC 92255T = LMG 32529T) is proposed.