Probiotic Therapy (BIO-THREE) Mitigates Intestinal Microbial Imbalance and Intestinal Damage Caused by Oxaliplatin.

Gastrointestinal mucositis associated with the use of chemotherapeutic drugs can seriously affect the quality of life of patients. In this study, a probiotic mixture, BIO-THREE, was used to alleviate intestinal damage caused by oxaliplatin in mice and human patients. Kunming mice were injected with 15 mg/kg of oxaliplatin twice, and BIO-THREE tablets were administered to mice for 12 days. Patients with gastric cancer undergoing oxaliplatin treatment took BIO-THREE tablets for 2 weeks. The changes in the composition of fecal microbiota both in patients and mice were analyzed using 16S rRNA high-throughput sequencing. In mice, oxaliplatin caused a drop in body weight and produced lesions in the liver and small intestines. Probiotic therapy successfully mitigated the damage caused by oxaliplatin to the intestinal tract, but it was not very effective for the liver damage and weight loss caused by oxaliplatin. The sequencing of the gut microflora indicated that oxaliplatin treatment increased the abundance of Bacteroidetes and decreased the abundance of Prevotella in mice. After taking probiotics, the feces of mice and human patients both had a higher abundance of Plovitella and a lower abundance of Bacteroides. The increase in Bacteroidetes and decrease in Prevotella in the gut community might be associated with oxaliplatin-induced intestinal damage. Probiotics appeared to be beneficial, decreasing intestinal damage by restoring the abundance of Bacteroidetes and Prevotella.

Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov.

A novel Gram-staining positive, aerobic, rod-shaped, non-motile and yellow-pigmented actinobacterium, designated strain WY83T, was isolated from a marine sediment of Indian Ocean. Strain WY83T grew optimally at 30-35 °C, pH 7-8 and with 0-3% (w/v) NaCl. The predominant menaquinones were MK-10, MK-11 and MK-12, and the major fatty acids were C19:1 ω9c/C19:1 ω11c, anteiso-C15:0, C17:0 3OH, and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The cell-wall peptidoglycan contained lysine as a diamino acid. The DNA G + C content was 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and ninety-two bacterial core genes indicated that strain WY83T formed an evolutionary lineage with Chryseoglobus frigidaquae JCM 14730T, Chryseoglobus indicus CTD02-10-2T, Yonghaparkia alkaliphila JCM 15138T, Microcella alkaliphila DSM 18851T and Microcella putealis DSM 19627T within the radiation enclosing members of the family Microbacteriaceae. All pairwise percentage of conserved proteins between strain WY83T and the closely related phylogenetic neighbors were greater than 65%. The average nucleotide identity and in silico DNA-DNA hybridization values were both below the thresholds used for the delineation of a new species. On the basis of the evidence presented, strains WY83T, Y. alkaliphila JCM 15138T, C. frigidaquae JCM 14730T, M. alkaliphila DSM 18851T and M. putealis DSM 19627T should belong to different species of the same genus. Strain WY83T represents a novel species of the genus Microcella, for which the name Microcella flavibacter sp. nov. is proposed. The type strain is WY83T (= KCTC 39637T = MCCC 1A07099T). Furthermore, Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila were reclassified as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov., respectively.

Nesterenkonia sedimenti sp. nov., isolated from marine sediment.

A Gram-staining-positive actinobacteria strain, designated MY13T, was isolated from deep-sea sediment of the western Pacific Ocean and subjected to a taxonomic polyphasic investigation. Based on the results, cells were aerobic, irregular short rod, non-motile and non-spore-forming. Colonies were cream, circular, smooth, convex, opaque and 1.0-2.0 mm in diameter after growth on MZ2 medium at 40 °C for 72 h. Strain MY13T grew at 4-50 °C (optimum, 40 °C), pH 7-12 (pH 9) and 0.5-15% (w/v) NaCl (3.5%). The 16S rRNA gene sequence analysis revealed that strain MY13T is affiliated with the genus Nesterenkonia and closely related to Nesterenkonia populi GP10-3T (96.6%). Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) differentiated it from its closest relatives, with values ranging from 19.8% to 22.4% and 72.6% to 78.0%, respectively. Chemotaxonomic analysis showed that the major menaquinone of strain MY13T was MK-7; major cellular fatty acids were anteiso-C17:0, anteiso-C15:0 and iso-C16:0; whole-cell sugars were galactose and xylose; the peptidoglycan type was L-Lys-Gly-D-Asp; and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids, one unknown polar lipid and two unknown lipids. The G+C content of genomic DNA was 63.1 mol%. Based on the physiological, chemotaxonomic and phylogenetic data, strain MY13T is a novel species of the genus Nesterenkonia, for which the name Nesterenkonia sedimenti sp. nov. is proposed. The type strain is MY13T (= LMG 28111T = MCCC 1A09979T = JCM 19767T = CGMCC 1.12784T).

Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments.

During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5-99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2T, YB235T, and WO024T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235T, WO024T, and o2T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains' ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2T, YB235T and WO024T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2T = JCM 33844T = MCCC 1A09961T), Brevibacterium pigmenatum sp. nov. (type strain YB235T = JCM 33843T = MCCC 1A09842T) and Brevibacterium atlanticum sp. nov. (type strain WO024T = JCM 33846T = MCCC 1A16743T) are proposed.

Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria.

We have identified three Microbacterium strains, A18JL200T, NY27T, and WY121T, that produce C50 carotenoids. Taxonomy shows they represent three novel species. These strains shared < 98.5% 16S rRNA gene sequence identity with each other and were closely related to Microbacterium aquimaris JCM 15625T, Microbacterium yannicii JCM 18959T, Microbacterium ureisolvens CFH S00084T, and Microbacterium hibisci CCTCC AB 2016180T. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) showed differences among the three strains and from their closest relatives, with values ranging from 20.4% to 34.6% and 75.5% to 87.6%, respectively. These values are below the threshold for species discrimination. Both morphology and physiology also differed from those of phylogenetically related Microbacterium species, supporting that they are indeed novel species. These strains produce C50 carotenoids (mainly decaprenoxanthin). Among the three novel species, A18JL200T had the highest total yield in carotenoids (6.1 mg/L or 1.2 mg/g dry cell weight). Unusual dual isoprenoid biosynthetic pathways (methylerythritol phosphate and mevalonate pathways) were annotated for strain A18JL200T. In summary, we found strains of the genus Microbacterium that are potential producers of C50 carotenoids, but their genome has to be investigated further.

A rapid and efficient method for the extraction and identification of menaquinones from Actinomycetes in wet biomass.

BACKGROUND: Menaquinones are constituents of prokaryote cell membranes where they play important functions during electron transport. Menaquinone profiles are strongly recommended for species classification when proposing a new Actinomycetes taxon. Presently, the most widely used methods to determine menaquinones are based on freeze-dried cells. Taxonomic research in our lab has revealed that menaquinone concentrations are low for some species of the genus Microbacterium, leading to difficulties in identifying menaquinones. RESULTS: Menaquinones extracted using the novel lysozyme-chloroform-methanol (LCM) method were comparable in quality to those obtained using the Collins method, the most widely used method. All tested strains extracted via the LCM method showed higher concentrations of menaquinones than those extracted via the Collins method. For some Microbacterium strains, the LCM method exhibited higher sensitivity than the Collins method, and more trace menaquinones were detected with the LCM method than the Collins method. In addition, LCM method is faster than the Collins method because it uses wet cells. CONCLUSION: The LCM method is a simple, rapid and efficient technique for the extraction and identification of menaquinones from Actinomycetes.

Complete genome sequence of Streptomyces sp. HSG2 from rhizosphere soil of mangrove in Qingmei Gang, Sanya.

Streptomyces sp. HSG2 was isolated from rhizosphere soil of a mangrove forest sample at Qingmei Gang, Sanya. The complete genome sequence of the strain HSG2 was obtained using PacBio Sequel HGAP.4 and comprised of 5,282,528 base pairs with a 71.9 mol% G + C content, 4504 protein-coding genes, and 71 RNAs. An in-silico analysis confirmed that genes associated with polysaccharide hydrolyzation, hydrocarbon degradation, and aerobic denitrification were presented in the genome. We also identified 24 natural product biosynthetic gene clusters for secondary metabolites, including those for streptobactin and nystatin A1. The complete genome sequence indicated that Streptomyces sp. HSG2 will provide insight into the biosynthesis and regulatory mechanisms for its secondary metabolites, and propose a potential use in biotechnological and novel bioactive natural product biosynthetic applications.

Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment.

Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide hydrolyzation, nitrite reduction, and phenol degradation. Multiple natural product biosynthesis gene clusters were identified as well. The complete genome sequence will provide insight into the potential use of this strain in biotechnological and natural product biosynthesis applications.

Chryseoglobus indicus sp. nov., isolated from deep sea water.

A novel Gram-stain-positive, motile, aerobic, non-spore-forming and slender rod-shaped actinobacterium, designated strain CTD02-10-2T, was isolated from deep sea water of the Indian Ocean. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CTD02-10-2T was grouped into a separated branch with Chryseoglobus frigidaquae JCM 14730T (98.4 % nucleotide sequence identity). The respiratory quinones were menaquinones with 11, 12, 13 and 14 isoprene units and anteiso-C15 : 0, iso-C16 : 0, anteiso-C15 : 1 A and anteiso-C17 : 0 were the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and three unknown glycolipids. The genome of strain CTD02-10-2T was 2.59 Mb, with a DNA G+C content of 69.6 mol% and contained genes involved in the biosynthesis of alkylresorcinol, ansamycin, and carotenoids. In silico DNA-DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between strain CTD02-10-2T and C. frigidaquae JCM 14730T were clearly below the thresholds used for the delineation of a new species. Based on its morphological and chemotaxonomic characteristics, as well as genotypic data, strain CTD02-10-2T was classified as a novel species of the genus Chryseoglobus, for which the name Chryseoglobus indicus sp. nov. is proposed. The type strain is CTD02-10-2T (=JCM 33842T=MCCC 1A16619T).

Brevibacterium profundi sp. nov., isolated from deep-sea sediment of the Western Pacific Ocean.

A new Gram-stain-positive, aerobic, non-motile and rod-shaped actinobacterium, designated O1T, was isolated from a deep-sea sediment of the Western Pacific Ocean. Strain O1T showed optimal growth at 30 °C, between pH 6.0 and 8.0, and in the presence of 1-5 % (w/v) NaCl. The predominant menaquinone was MK-8 (H2), and anteiso-C15 : 0 and anteiso-C17 : 0 were the major fatty acids. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid. The DNA G+C content of strain O1T was 64.9 mol% and the genome size was 4.17 Mb. Based on a similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain O1T belonged to the genus Brevibacterium. The values of average nucleotide identity and in silico DNA-DNA hybridization between strain O1T and its close relatives were well below the thresholds used for the delineation of a new species. On the basis of the morphological and chemotaxonomic characteristics, as well as the genotypic data, it is proposed that strain O1T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium profundi sp. nov. is proposed. The type strain is O1T (=JCM 33845T=MCCC 1A16744T).

Saccharopolyspora coralli sp. nov. a novel actinobacterium isolated from the stony coral Porites.

A novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain E2AT, was isolated from a coral sample and examined using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain E2AT formed a distinct phyletic lineage in the genus Saccharopolyspora and was closely related to S. cavernae CCTCC AA 2012022T (96.4 %) and S. lacisalsi CCTCC AA 2010012T (95.3 %). The isolate grew at 15-35 °C, pH 5-12 and in the presence of 1-16 % (w/v) NaCl. The cell-wall diamino acid was meso-DAP. Major fatty acids identified were iso-C15 : 0, iso-C16 : 0 and C17 : 1 ω8c. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified glycolipid, one unidentified phospholipid and one unidentified aminolipid. The genomic DNA G+C content was 68.6 mol%. Based on the data from the polyphasic taxonomic study reported here, strain E2AT represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora coralli sp. nov. is proposed. The type strain is E2AT=(JCM 31844T=MCCC 1A17150T).

Nesterenkonia salmonea sp. nov. and Nesterenkonia sphaerica sp. nov., isolated from the Southern Atlantic Ocean.

Two Gram-positive, aerobic, non-motile and non-spore-forming actinobacteria, strains GY074T and GY239T, were isolated from deep-sea sediment of the Southern Atlantic Ocean. The results of phylogenetic analysis of 16S rRNA gene sequences placed both isolates within the genus Nesterenkonia, and showed a sequence similarity of 98.3 % between the two strains and similarites of 94.3-97.2 % with respect to Nesterenkonia species with validly published names. Based on whole-genome sequences, the values of in silico DNA-DNA hybridization and the average nucleotide identity between strains GY074T and GY239T were 21.2 and 78.1 %, respectively, less than the proposed cut-off level for species delineation, i.e. 70 and 95 %. For both strains, the major cellular fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0, and the major menaquinones were MK-7, MK-8 and MK-9. The major polar lipid contents of the two strains were similar with phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C contents of strains GY074T and GY239T were 61.1 and 64.2 mol%, respectively. On the basis of the phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent two novel species of the genus Nesterenkonia, for which the names Nesterenkonia salmonea sp. nov. (type strain GY074T=KCTC 39639T=MCCC 1A11256T) and Nesterenkonia sphaerica sp. nov. (type strain GY239T=KCTC 39640T=MCCC 1A10688T) are proposed.

Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment.

A Gram-stain-negative, short rod-shaped, non-motile, catalase- and oxidase-positive, aerobic bacterium, designated GY0581T, was isolated from marine sediment sampled from the Western Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain GY0581T belonged to the genus Paracoccus and had the highest levels of sequence similarity to Paracoccus sediminis JCM 18467T (98.2 %). Levels of similarity between strain GY0581T and other Paracoccus species were lower than 97.0 %. The average nucleotide identity and the DNA-DNA hybridization values between strain GY0581T and P. sediminis JCM 18467T were 83.9 and 27 %, respectively, which are below the respective thresholds for species differentiation. The major cellular fatty acid was C18 : 1ω7c (79.5 %). The only isoprenoid quinone was Q-10. The polar lipid pattern indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, three unidentified phospholipids, three unidentified aminolipids, one unidentified glycolipid and two unidentified lipids. The DNA G+C content of strain GY0581T was 65.6 mol%. On the basis of polyphasic characterization, it is concluded that strain GY0581T represents a novel species of the genus Paracoccus, for which the name Paracoccus subflavus sp. nov. is proposed. The type strain is GY0581T (=KCTC 42710T=MCCC 1A10575T).

Gut remediation: a potential approach to reducing chromium accumulation using Lactobacillus plantarum TW1-1.

Some lactobacilli have protective effects against some heavy metals in mammals, but the underlying mechanism is not fully understood. To evaluate the remediation potency and the mechanism of Lactobacillus against chromium (Cr) in mice, Lactobacillus plantarum TW1-1 was orally administrated to Kunming mice for 7 weeks during exposure to 1 mM K2Cr2O7 in drinking water. Results showed that TW1-1 helped to decrease Cr accumulation in tissues and increase Cr excretion in feces, and may also attenuate alterations in oxidative stress and histopathological changes caused by Cr exposure. Moreover, the chromate reduction ability of fecal bacteria doubled after administration of TW1-1 upon Cr induction. MiSeq sequencing of fecal bacterial 16S rRNA genes revealed that the overall structures of gut microbiota was shifted by Cr exposure and partially restored by TW1-1. The abundances of 49 of the 79 operational taxonomic units altered by Cr were reversed by TW1-1. Based on these, we proposed a working model of TW1-1 against Cr: TW1-1 helps to remove Cr from the host and meanwhile acts as a regulator of gut microbiota, which aids in chromate reduction and provide protection against Cr. We call this process of remediation of heavy metal in the gut "gut remediation".

[Expression and clinical significance of cyclooxygenase-2 in nasal and paranasal sinus carcinoma].

OBJECTIVE: To investigate the relationship between the expression of cyclooxygenase-2 (COX-2) and the carcinogenesis and invasive behavior of nasal and paranasal sinus carcinoma (NPSC). METHOD: The expression of COX-2 were detected in 69 case NPSC tissues, paracancerous atypical hyperplasia tissue and normal tissue by using immunohistochemical techniques of SP method. RESULT: The positive rate of COX-2 in NPSC tissues and atypical hyperplasia tissue and normal tissue was 65.22% and 42.31% and 3.33%, respectively. The positive rate of COX-2 in NPSC tissues was significantly higher than that in normal tissue (P < 0.01), and increased apparently with the lesion progressing from normal to atypical hyperplasia tissue to NPSC tissues, and also correlated with the increasing of tumor (P < 0.05). CONCLUSION: COX-2 may play an important role in the carcinogenesis and invasion of NPSC.