Labrys wisconsinensis sp. nov., a budding bacterium isolated from Lake Michigan water, and emended description of the genus Labrys

Description of Labrys sedimenti sp. nov., isolated from a diclofenac-degrading enrichment culture, and genome-based reclassification of Labrys portucalensis as a later heterotypic synonym of Labrys neptuniae

A Gram-stain-negative strain, designated as Zidic-5T, was isolated from diclofenac-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain Zidic-5T belongs to the genus Labrys, with the highest 16S rRNA gene similarity to Labrys neptuniae LMG 23578T (99.13%), followed by Labrys portucalensis F11T (99.06%), Labrys methylaminiphilus JLW10T (98.58%) and Labrys okinawensis DSM 18385T (98.32%). The draft genome sequence of strain Zidic-5T is 7.64 Mb long, and the G+C content of the genome is 63.5 mol%. The orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain Zidic-5T and its closest relatives were below the threshold values for species demarcation, confirming that strain Zidic-5T is distinctly separated from its closest relatives. Additionally, comparative whole-genome analysis of type strains of L. neptuniae and L. portucalensis indicated that they belong to the same genomic species, suggesting that L. portucalensis is a later heterotypic synonym of L. neptuniae. Cells of strain Zidic-5T were strictly aerobic, coccoid-shaped and non-motile. The predominant fatty acids (>10% of the total) of strain Zidic-5T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω7c. The major ubiquinone of strain Zidic-5T was Q-10, while the major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on the polyphasic study, it is concluded that strain Zidic-5T represents a novel species of the genus Labrys; thus, the name of Labrys sedimenti sp. nov. is proposed. The type strain of the species is strain Zidic-5T (=LMG 33565T=NCAIM B.02686T).

Removal of Ibuprofen in Water by Bioaugmentation with Labrys neptuniae CSW11 Isolated from Sewage Sludge-Assessment of Biodegradation Pathway Based on Metabolite Formation and Genomic Analysis

Ibuprofen (IBP) is one of the most consumed drugs in the world. It is only partially removed in wastewater treatment plants (WWTPs), being present in effluent wastewater and sewage sludge, causing the widespread introduction of IBP as an emergent xenobiotic in different environmental compartments. This study describes the use of Labrys neptuniae CSW11, recently described as an IBP degrader, through bioaugmentation processes for the removal of IBP from water under different conditions (additional carbon sources, various concentrations of glucose and IBP). L. neptuniae CSW11 showed very good results in a wide range of IBP concentrations, with 100% removal in only 4 days for 1 and 5 mg L-1 IBP and 7 days for 10 mg L-1, and up to 48.4% removal in 28 days for IBP 100 mg L-1 when using glucose 3 g L-1 as an additional carbon source. Three IBP metabolites were identified during the biotransformation process: 1-hydroxyibuprofen (1-OH-IBP), 2-hydroxyibuprofen (2-OH-IBP), and carboxyibuprofen (CBX-IBP), whose concentrations declined drastically in the presence of glucose. IBP metabolites maintained a certain degree of toxicity in solution, even when IBP was completely removed. The results indicate that L. neptuniae CSW11 can be quite effective in degrading IBP in water, but the bioaugmentation method should be improved using CSW11 in consortia with other bacterial strains able to degrade the toxic metabolites produced. A genome-based analysis of L. neptuniae CSW11 revealed different enzymes that could be involved in IBP biodegradation, and a potential metabolic pathway was proposed based on the metabolites observed and genome analysis.

Coordinated response of milk bacterial and metabolic profiles to subacute ruminal acidosis in lactating dairy cows

BACKGROUND

Bovine milk is an important source of nutrition for human consumption, and its quality is closely associated with the microbiota and metabolites in it. But there is limited knowledge about the milk microbiome and metabolome in cows with subacute ruminal acidosis.

METHODS

Eight ruminally cannulated Holstein cows in mid lactation were selected for a 3-week experiment. The cows were randomly allocated into 2 groups, fed either a conventional diet (CON; 40% concentrate; dry matter basis) or a high-concentrate diet (HC; 60% concentrate; dry matter basis).

RESULTS

The results showed that there was a decreased milk fat percentage in the HC group compared to the CON group. The amplicon sequencing results indicated that the alpha diversity indices were not affected by the HC feeding. At the phylum level, the milk bacteria were dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes both in the CON and HC groups. At the genus level, the HC cows displayed an improved proportion of Labrys (P = 0.015) compared with the CON cows. Results of both the principal components analysis and partial least squares of discriminant analysis of milk metabolome revealed that samples of the CON and HC groups clustered separately. A total of 31 differential metabolites were identified between the two groups. Of these, the levels of 11 metabolites decreased (α-linolenic acid, prostaglandin E2, L-lactic acid, L-malic acid, 3-hydroxysebacic acid, succinyladenosine, guanosine, pyridoxal, L-glutamic acid, hippuric acid, and trigonelline), whereas the levels of the other 20 metabolites increased in the HC group with respect to the CON group (P < 0.05).

CONCLUSION

These results suggested that subacute ruminal acidosis less impacted the diversity and composition of milk microbiota, but altered the milk metabolic profiles, which led to the decline of the milk quality.

Identification of tissue-specific microbial profile of esophageal squamous cell carcinoma by full-length 16S rDNA sequencing

It was previously believed that the microbial community in the esophagus was relatively stable, but it has been reported that different esophageal diseases have different microbial community characteristics. In this study, we recruited patients with esophageal squamous cell carcinoma (ESCC) and collected 51 pairs of tumor and adjacent non-tumor tissues for full-length 16S rDNAsequencing and qPCR to compare the differences in microbial community structure. The results of sequencing in 19 pairs of tissues showed that Proteobacteria, Firmicutes, Bacteroidetes, Deinococcus-Thermus, and Actinobacteria were the main bacteria in tumor and adjacent non-tumor tissues. At the genus level, the bacteria with the highest relative proportion in tumor and adjacent non-tumor tissues were Streptococcus and Labrys, respectively. At the same time, it was observed that the complexity of microbial interactions in tumor tissues was weaker than that of adjacent non-tumor tissues. The results also found that the relative abundance of 24 taxa was statistically different between tumor and adjacent non-tumor tissues. The findings of qPCR in 32 pairs of tissues further evidence that the relative proportions of Blautia, Treponema, Lactobacillus murinus, Peptoanaerobacter stomatis, and Fusobacteria periodonticum were statistically different in tumor and adjacent non-tumor tissues. The findings of PIRCUSt2 indicated the lipopolysaccharide biosynthesis and biotin metabolism in the microbiome of cancer tissues are more significant. This study supplements the existing information on the structure, function, and interaction of microorganisms in the esophagus in situ and provides a direction for the further exploration of the relationship between esophageal in situ microorganisms and esophageal squamous cell carcinoma. KEY POINTS: • The structure of the microbial community in esophageal cancer tissue and adjacent non-tumor tissues at the phylum level is similar • Streptococcus and Labrys are the most important bacteria in esophageal tumor tissues and adjacent non-tumor tissues, respectively • Microbial interactions in tumor tissues are stronger than in adjacent non-tumor tissues.

Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae

L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria-nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.

Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water

Three strains of a Gram-stain negative bacterium were isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1131 had sequence similarities to Bosea vaviloviae LMG 28367^T, Bosea lathyri LMG 26379^T, Bosea lupini LMG 26383^T, Bosea eneae CCUG 43111^T, Bosea vestrisii CCUG 43114^T and Boseamassiliensis CCUG 43117^T of 99.8, 99.1, 98.4, 98.4, 98.4 and 98.2 %, respectively. The average nucleotide identity value between strain 1131^T and Bosea vaviloviae Vaf-18^T was 93.4 % and the DNA relatedness was 38 %. The primary cellular fatty acids of strain 1131^T were C16 : 1ω7c and C18 : 1ω7c. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major compound in the quinone system was ubiquinone Q-10 and in the polyamine pattern sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 5-35 °C, pH values of pH 5.5-8.0, a salt tolerance range of 0.0-1.2 % (w/v), and production of an unknown water soluble brown pigment. After phenotypic, chemotaxonomic and genomic analyses, this isolate was identified as a novel species for which the name Bosea psychrotolerans is proposed. The type strain is 1131^T (NRRL B-65405=LMG 30034).

Phytohormone production endowed with antagonistic potential and plant growth promoting abilities of culturable endophytic bacteria isolated from Clerodendrum colebrookianum Walp

In this study, culturable endophytic bacterial isolates obtained from an ethnomedicinal plant Clerodendrum colebrookianum Walp., were assessed for their diversity, in vitro screening for their plant growth promoting (PGP) activities and to use them as inoculant for in vivo PGP activities with biocontrol potential. Totally, 73 isolates were recovered from different tissues of C. colebrookianum were identified by 16S rRNA gene sequencing and phylogenetically analyzed by using BOX-PCR fingerprinting. Out of 73 isolates, 52 exhibited varying extents of antagonistic potential were selected for screening for various PGP traits. Concerning the PGP activities, the percentage of isolates positive for P-solubilisation, indolic compounds production, siderophore and ammonia production were 84.6, 92.3, 78.8 and 98.0 respectively. All isolates were positive for the production of hydrocyanic acid (HCN) and 86.5%, 84.6% and 90.3% of isolates showed significant cellulase, amylase and protease production respectively. Further, the top 10 bacterial isolates based on a bonitur scale with multiple PGP activities were screened for root surface colonization and biofilm formation ability. Out of selected 10 isolates, 9 showed significant potential for root surface colonization on tomato roots. Isolate BPSAC6 identified as Bacillus sp. was most efficient in biofilm formation as assessed with respect to the intensity of crystal violet, which further showed their potential to withstand various biotic and abiotic stresses. Furthermore, Bacillus sp. strain BPSAC6 showed a significant increase in shoot and root height as well as fresh weight after 45 and 60 d of inoculation with tomato seedlings. Additionally, biosynthetic potential of antagonistic isolate was detection by using PKSI, PKSII and NRPS biosynthetic genes. Two isolates Pseudomonas psychrotolerans and Labrys wisconsinensis were reported first time as an endophyte. At last, first time an endophytic bacterial strain Bacillus sp. BPSAC6 was reported to produce altogether three phytohormones (IAA, Kinetin and 6-Benzyladenine). This study is the first report that bacteria isolated from C. colebrookianum has biocontrol as well as PGP abilities endowed with phytohormones production and can be used for the preparation of bioinoculant for plant growth promotion.

Labrys soli sp. nov., isolated from the rhizosphere of ginseng

In this study, we describe strain DCY64T that was isolated from the rhizosphere of three-year-old Korean ginseng root. Cells were Gram-reaction negative, oxidase- and catalase-positive, strictly aerobic, capsulated, non-motile, non-sporulating and spherical to short rod-shaped. Multiplicative budding cells were produced. Vesicles covered the surface of cells. Phylogenetic analysis placed strain DCY64T within the genus Labrys with the highest similarity to Labrys monachus VKM B-1479T (97.6 % 16S rRNA gene sequence similarity), followed by Labrys okinawensis MAFF 210191T (97.5 %), Labrys miyagiensis G24103T (97.4) and Labrys portucalensis F11T (97.0 %). The genomic DNA G+C content was 63 mol%. The presences of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 1 cyclo ω8c and C16 : 0 as major fatty acids; phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol as major polar lipids; ubiquinone Q-10 as the predominant quinone and sym-homospermidine as the dominant polyamine were found in strain DCY64T. These chemotaxonomic results were in accordance with those of members of the genus Labrys. However, the absence of C16 : 0 2-OH, C16 : 0 3-OH and C18 : 1 2-OH from the fatty acids profile and differences in minor polar lipids and phenotypic characteristics distinguished strain DCY64T from the closest type strains. The discrimination was also supported by unique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) fingerprints, as well as DNA-DNA hybridization values ( ≤ 48 %) between strain DCY64T and related type strains. Therefore, we propose that strain DCY64T represents a novel species of the genus Labrys. The name Labrys soli sp. nov. is proposed, with DCY64T ( = KCTC 32173T = JCM 19895T) as the type strain.

Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water

A mesophilic bacterium appearing as curved rod-shaped cells was isolated from Lake Michigan water. It exhibited highest similarities with Sediminibacterium ginsengisoli DCY13T (94.4 %); Sediminibacterium salmoneum NJ-44T (93.6 %) and Hydrotalea flava CCUG 51397 T (93.1 %) while similarities with other recognized species were <92.0 %. The primary polar lipid was phosphatidylethanolamine, with moderate amounts of two unidentified glycolipids, three unknown polar lipids, one unknown aminophospholipid and one aminolipid. The primary respiratory quinone was MK-7 and sym-homospermidine was the primary polyamine. The major cellular fatty acids were iso-C15 : 1G, iso-C15 : 0, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH, with moderate amounts of iso-C16 : 0. The presence of glycolipids differentiated the novel strains from related genera. The DNA mol% G+C content of the type strain MU-2T was 45.2. Results for other phenotypic and molecular analyses indicated that strain MU-2T is a representative of a novel genus and species for which the name Vibrionimonas magnilacihabitans is proposed. The type strain is MU-2T ( = NRRL B-59231 = DSM 22423).

Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water

A psychrophilic, Gram-negative bacterium, designated MOL-1T, was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1T has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of Sphingobacterium shayense HS39T, S. lactis WCC 4512T, S. composti T5-12T, S. daejeonense TR6-04T, S. bambusae IBFC2009T and S. alimentarium WCC 4521T. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1T represents a novel Sphingobacterium species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1T ( = NRRL B-59232T  = DSM 22418T).