Pseudomonas hutmensis sp. nov., a New Fluorescent Member of Pseudomonas putida Group

Draft genome for Pseudomonas alkylphenolica IMGN1, isolated from soil

Biocontrol using organisms like Pseudomonas alkylphenolica offers a viable alternative to chemical pesticides, enhancing plant growth and reducing environmental impact. This study details the genome of Pseudomonas alkylphenolica IMGN1, a strain known for promoting plant growth, advancing our understanding of biocontrol mechanisms.

Human milk microbial species are associated with infant head-circumference during early and late lactation in Guatemalan mother-infant dyads

Human milk contains abundant commensal bacteria that colonize and establish the infant's gut microbiome but the association between the milk microbiome and head circumference during infancy has not been explored. For this cross-sectional study, head-circumference-for-age-z-scores (HCAZ) of vaginally delivered breastfed infants were collected from 62 unrelated Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala during two stages of lactation, 'early' (6-46 days postpartum, n = 29) or 'late' (109-184 days postpartum, n = 33). At each stage of lactation, infants were divided into HCAZ ≥ -1 SD (early: n = 18; late: n = 14) and HCAZ < -1 SD (early: n = 11; late: n = 19). Milk microbiome communities were assessed using 16S ribosomal RNA gene sequencing and DESeq2 was used to compare the differential abundance (DA) of human milk microbiota with infant HCAZ subgroups at both stages of lactations. A total of 503 ESVs annotated 256 putative species across the 64 human milk samples. Alpha-diversity using Chao index uncovered a difference in microbial community richness between HCAZ ≥ -1 SD and HCAZ < -1 SD groups at late lactation (p = 0.045) but not at early lactation. In contrast, Canonical Analysis of Principal Coordinates identified significant differences between HCAZ ≥ -1 SD and HCAZ < -1 SD at both stages of lactation (p = 0.003); moreover, 26 milk microbial taxa differed in relative abundance (FDR < 0.05) between HCAZ ≥ -1 SD and HCAZ < -1 SD, with 13 differentially abundant at each lactation stage. Most species in the HCAZ ≥ -1 SD group were Streptococcus species from the Firmicutes phylum which are considered human colonizers associated with human milk whereas the HCAZ < -1 SD group at late lactation had more differentially abundant taxa associated with environmentally and 'potentially opportunistic' species belonging to the Actinobacteria genus. These findings suggest possible associations between brain growth of breastfed infants and the milk microbiome during lactation. Importantly, these data provide the first evidence of cross talk between the human milk microbiome and the infant brain that requires further investigation.

Pseudomonas allokribbensis sp. nov. and Pseudomonas gozinkensis sp. nov., Two New Species Isolated from a Volcanic Island, Izu Oshima, Japan

The genomes of two Pseudomonas strains, IzPS23^T and IzPS32d^T isolated from soil samples of Izu Oshima were compared to Pseudomonas type strains. Whole-genome sequence analysis revealed both belong to the Pseudomonas fluorescens lineage. The average nucleotide identity values of the whole-genome sequences of IzPS23^T and IzPS32d^T compared with other type strains showed high correlations with Pseudomonas kribbensis (93.1%) and Pseudomonas glycinae (93.5%), respectively. Genome-to-genome distances between the whole-genome sequences of IzPS23^T and IzPS32d^T showed correlations with Pseudomonas kribbensis (51.0%) and Pseudomonas glycinae (53.2%), respectively. Genotypic and phenotypic analysis indicated the two strains were novel species, and were named Pseudomonas allokribbensis (IzPS23^T = CECT 9961^T, = LMG 31525^T) and Pseudomonas gozinkensis (IzPS32d^T = CECT 9962^T, = LMG 31526^T), respectively.

Co-cultivation of Beta vulgaris limits the pre-harvest colonization of foodborne pathogen (Salmonella spp.) on tomato

Soil-borne Salmonella is associated with a large number of food-related disease outbreaks linked to pre-harvest contamination of plants (like tomato) in agricultural fields. Controlling the spread of Salmonella at field is very important in order to prevent various food-borne illnesses. One such approach involves the utilization of antimicrobial secondary metabolite of plant origin. We screened common salad vegetables for anti-Salmonella activity. Beta vulgaris root (beetroot) had very low colonization of Salmonella under in vitro conditions. We hypothesized that beetroot can be used to reclaim the soil contaminated with Salmonella. Cultivation of B. vulgaris in Salmonella treated soil brings down its CFU significantly. Since these antimicrobial effects are non-specific, a co-cultivation system of beet and tomato (a Salmonella susceptible plant) was used to analyze the effect on soil and its microbiota. The soil physicochemical properties and bacterial diversity were unaffected when tomato and beet co-cultivation was used. However, Salmonella burden on the tomato was reduced and its yield was restored. Thus, the inclusion of these crops in the crop-rotation or as a mixed/intercrop or as a bio-control crop can be a fruitful tool to reclaim the Salmonella contaminated soil.

Pseudomonas izuensis sp. nov., a novel species isolated from Izu Oshima, Japan

An aerobic, Gram-stain-negative, rod-shaped bacterial strain, IzPS43_3003^T, was isolated from Izu Oshima, an active volcanic island located 22 km east of the Izu Peninsula, Japan. The sequence of its 16S rRNA gene indicated that IzPS43_3003^T belongs to the Pseudomonas fluorescens lineage, with its sequence being most similar to that of Pseudomonas vancouverensis DhA-51^T (99.79 %). Phylogenetic analysis based on whole genome sequences showed that IzPS43_3003^T was a member of the Pseudomonas jessenii subgroup. The average nucleotide identity values and genome-to genome distances between the whole genome sequences of IzPS43_3003^T and other type strains showed that the highest correlations were with Pseudomonas moorei DSM 12647^T (87.3 and 33.5% respectively). These genotypic and phenotypic analyses indicated that IzPS43_3003^T belongs to a novel species, Pseudomonas izuensis sp. nov. Its type strain is IzPS43_3003^T (=LMG 31527^T,=CECT 9963^T).

Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively

This study was conducted to clarify the taxonomic status of the species Pseudomonas fuscovaginae and Pseudomonas shirazica . Whole genome sequences for the type strains of P. fuscovaginae and P. shirazica were compared against the closely related type strains of the Pseudomonas putida group and the Pseudomonas fluorescens group species. Average nucleotide identity and digital DNA–DNA hybridization values between P. fuscovaginae LMG 2158T and Pseudomonas asplenii ATCC 23835T were 98.4 and 85.5 %, and between P. shirazica VM14T and Pseudomonas asiatica RYU5T were 99.3 and 95.3 %. These values were greater than recognized thresholds for bacterial species delineation, indicating that they belong to the same genomospecies, respectively. Therefore, P. fuscovaginae and P. shirazica should be reclassified as later heterotypic synonyms of P. asplenii and P. asiatica , respectively.