Lactobacillus psittaci sp. nov., isolated from a hyacinth macaw (Anodorhynchus hyacinthinus)

Lactobacillus corticis sp. nov., isolated from hardwood bark

During a study on the biodiversity of bacteria that inhabit woody biomass, we isolated a strain coded B40^T from hardwood bark used as a compost ingredient in Japan. The strain, characterized as B40^T, is a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative bacterium. This novel isolate showed growth at 30-50 °C, at pH 3.5-7.5 and in the presence of up to 4 % (w/v) NaCl. Its major fatty acids include C_16:0, C_18:1 ω9c and summed feature 8. The genomic DNA G+C content of strain B40^T is 42.2 mol%. Results of 16S rRNA gene sequence-based phylogenetic analysis indicated that strain B40^T belongs to the genus Lactobacillus and the closest neighbours of strain B40^T are Lactobacillus gigeriorum 202^T (95.7 %), Lactobacillus pasteurii CRBIP 24.76^T (95.6 %), Lactobacillus psittaci DSM 15354^T (95.4 %), Lactobacillus fornicalis TV1018^T (95.4 %) and Lactobacillus jensenii ATCC 25258^T (95.2 %). The amino acid sequence-based phylogenetic analyses of 489 shared protein-encoding genes showed that the strain forms a phylogenetically independent lineage in the genus Lactobacillus but could not be assigned to any known species. Strain B40^T has an average nucleotide identify of <70.2 % and a digital DNA-DNA hybridization value of 19.2 % compared with the strains of other closely related Lactobacillus species. Differential genomic, phenotypic and chemotaxonomic properties, in addition to phylogenetic analyses, indicated that strain B40^T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus corticis sp. nov. is proposed. The strain type is B40^T (=JCM 32597^T=DSM 107967^T).

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group

One Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, and coccobacilli-shaped strain, designated c10Ua161MT, was isolated from a urine sample from a reproductive-age healthy woman. Comparative 16S rRNA gene sequence analysis indicated that strain c10Ua161MT belonged to the genus Lactobacillus . Phylogenetic analysis based on pheS and rpoA gene sequences strongly supported a clade encompassing strains c10Ua161MT and eight other strains from public databases, distinct from currently recognized species of the genus Lactobacillus. In silico Average Nucleotide Identity (ANI) and Genome-to-Genome Distance Calculator (GGDC), showed 87.9 and 34.3 % identity to the closest relative Lactobacillus jensenii , respectively. The major fatty acids of strain c10Ua161MT were C18 : 1ω9c (65.0%), C16 : 0 (17.8%), and summed feature 8 (10.2 %; comprising C18 : 1ω7c, and/or C18 : 1ω6c). The DNA G+C content of the strains is 34.2 mol%. On the basis of data presented here, strain c10Ua161MT represents a novel species of the genus Lactobacillus , for which the name Lactobacillus mulieris sp. nov. is proposed. The type strain is c10Ua161MT (=CECT 9755T=DSM 108704T).

Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing

Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.

Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota

The genus Lactobacillus includes over 215 species that colonize plants, foods, sewage and the gastrointestinal tract (GIT) of humans and animals. In the GIT, Lactobacillus population can be made by true inhabitants or by bacteria occasionally ingested with fermented or spoiled foods, or with probiotics. This study longitudinally surveyed Lactobacillus species and strains in the feces of a healthy subject through whole genome sequencing (WGS) data-mining, in order to identify members of the permanent or transient populations. In three time-points (0, 670 and 700 d), 58 different species were identified, 16 of them being retrieved for the first time in human feces. L. rhamnosus, L. ruminis, L. delbrueckii, L. plantarum, L. casei and L. acidophilus were the most represented, with estimated amounts ranging between 6 and 8 Log (cells g(-1) ), while the other were detected at 4 or 5 Log (cells g(-1) ). 86 Lactobacillus strains belonging to 52 species were identified. 43 seemingly occupied the GIT as true residents, since were detected in a time span of almost 2 years in all the three samples or in 2 samples separated by 670 or 700 d. As a whole, a stable community of lactobacilli was disclosed, with wide and understudied biodiversity.

Chronic dermatitis caused by Lactobacillus jensenii infection in a blue and gold macaw (Ara ararauna)

CASE DESCRIPTION

A 5-year-old sexually intact female blue and gold macaw (Ara ararauna) was evaluated because of a swelling on the right side of the face and irritated area on the ventral aspect of the keel.

CLINICAL FINDINGS

Clinical findings were consistent with dermatitis (right facial lesion) and a coalescing subdermal granuloma (ventral keel lesion). Hematologic analysis revealed monocytosis and mild anemia. Histologic evaluation of the ventral keel lesion revealed evidence of chronic heterophilic dermatitis with multinucleated giant cells and bacterial rods and cocci. An unspeciated gram-positive rod-shaped bacterium was isolated via aerobic bacterial culture. Results of bacterial biochemical tests suggested the organism was a type of Actinomyces. A 16S rRNA gene sequence analysis was performed; results indicated the organism was Lactobacillus jensenii.

TREATMENT AND OUTCOME

Extensive surgical debridement of the branching granuloma, which extended throughout the length of the keel, followed by long-term treatment with ciprofloxacin and clindamycin provided full resolution of clinical signs. No recrudescence of clinical signs was evident for up to 18 months after the initial evaluation.

CLINICAL RELEVANCE

To the authors' knowledge, this is the first report of Lactobacillus-associated dermatitis or subdermal granuloma in the scientific literature and the second report of L jensenii in avian species. Use of 16S rRNA gene sequence analysis was instrumental in the identification of this fastidious organism, indicating the method's usefulness as a diagnostic tool.

Lactic acid bacteria in marinades used for modified atmosphere packaged broiler chicken meat products

Lactic acid bacteria (LAB) in some marinades commonly used in Finland for modified atmosphere packaged poultry meat products were enumerated and identified to determine whether the marinades contained LAB species that cause meat spoilage. The concentrations of LAB in 51 marinade samples ranged from less than 100 to 8.0 x 10(5) CFU/ml. Seventeen of the samples produced LAB growth only after enrichment, and in five samples no growth was detected either by direct culturing or enrichment. Eighty-eight randomly selected isolates, 51 from the enumerated plates and 37 from enriched samples, were identified using a database of 16S and 23S rRNA gene HindIII restriction fragment length polymorphism patterns of over 300 type and references LAB strains as operational taxonomic units in numerical analyses. The predominating LAB in the enumerated samples was Lactobacillus plantarum (25 of 51 isolates). Eleven isolates were identified as Lactobacillus paracasei subsp. paracasei, and nine were Lactobacillus parabuchneri. None of these species are considered specific spoilage LAB in marinated modified atmosphere packaged poultry meat products nor have they been reported to dominate in unspoiled late-shelf-life products. These results indicate that even though marinades may contain high numbers of LAB, they are not necessarily sources of specific meat spoilage LAB. Therefore, risks associated with meat quality are not predicted by quantitative enumeration of LAB in marinades.