Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov., isolated from the preen glands of Great Spotted Woodpeckers (Dendrocopos major)

Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds

The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel's lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes. Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Airborne methicillin-resistant Staphylococcus aureus, other bacteria, fungi, endotoxin, and dust in a pigeon exhibition

Pigeon breeding is associated with exposure to airborne microorganisms and endotoxin and with symptoms of the airways. Antibiotic resistance is a threat to human health. Some pigeons participate in national and international indoor exhibitions. This study aims to obtain knowledge about the potential human exposure to dust, endotoxin, fungi, and bacteria including the methicillin-resistant Staphylococcus aureus (MRSA) in a pigeon exhibition in Denmark. In walking areas for visitors, airborne microorganisms in different size fractions able to enter the airways were sampled and following identified. The average concentrations were: 5000 cfu fungi/m³, 1.8 × 10⁴ cfu bacteria/m³, 37 endotoxin units/m³, and 0.18 mg dust/m³ air with the highest concentrations in-between rows with pigeon cages. The fungal species Wallemia sp. and Aspergillus versicolor and the bacterial species S. equorum and S. aureus were found in high concentrations. MRSA spa type t034 described to be associated with livestock was found in the air. Most of the S. aureus was present in the size fraction of 1.1-2.1 μm, which are particles able to enter the human terminal bronchi. In conclusion, fungi, bacteria, and endotoxin, respectively, were found in concentrations 10, 2000, and 200 times higher than outdoor references. The airborne bacteria in the exhibition were mainly species found previously in pigeon coops showing that the pigeons are the sources of exposure. The presence of airborne MRSA in the pigeon exhibition highlights the importance of also considering this environment as a potential place of exchange of resistant bacteria between animals and between animals and humans.

Microbial infection risk predicts antimicrobial potential of avian symbionts

Symbiotic bacteria on animal hosts can prevent pathogenic bacterial infections by several mechanisms. Among them, symbiotic bacteria can indirectly enhance host’s immune responses or, directly, produce antimicrobial substances against pathogens. Due to differences in life-style, different host species are under different risks of microbial infections. Consequently, if symbiotic bacteria are somewhat selected by genetically determined host characteristics, we would expect the antimicrobial properties of bacterial symbionts to vary among host species and to be distributed according to risk of infection. Here we have tested this hypothesis by measuring the antimicrobial ability of the bacterial strains isolated from the uropygial-gland skin of 19 bird species differing in nesting habits, and, therefore, in risk of microbial infection. In accordance with our predictions, intensity and range of antimicrobial effects against the indicator strains assayed varied among bird species, with hole-and open-nesters showing the highest and the lowest values, respectively. Since it is broadly accepted that hole-nesters have higher risks of microbial infection than open nesters, our results suggest that the risk of infection is a strong driver of natural selection to enhance immunocompetence of animals through selecting for antibiotic-producing symbionts. Future research should focus on characterizing symbiotic bacterial communities and detecting coevolutionary processes with particular antibiotic-producing bacteria within-host species.

Probiotic Characterization of Indigenous Kocuria flava Y4 Strain Isolated from Dioscorea villosa Leaves

This aim of the study was to isolate and screen potential probiotics from Dioscorea villosa leaves. The potential isolate Y4 was obtained from the Dioscorea villosa leaves, and its ability to grow in a medium containing high NaCl concentrations (2-10%) indicated its negative hemolytic activity. Furthermore, Y4 demonstrated inhibitory activity against human pathogens, such as Klebsiella pneumonia, Staphylococcus aureus, Citrobacter koseri, and Vibrio cholerae, as well as towards a plant pathogen isolate OR-2 (obtained from Citrus sinensis). Some biologically important functional groups of Y4 metabolites, such as sulfoxide; aliphatic ether; 1, 2, 3-trisubstituted, tertiary alcohol: vinyl ether; aromatic amine; carboxylic acid; nitro compound; alkene mono-substituted; and alcohol, were identified through FTIR analysis. The 16S rRNA sequencing and subsequent phylogenetic tree analysis indicated that Y4 and OR-2 are the closest neighbors to Kocuria flava (GenBank accession no. MT773277) and Pantoea dispersa (GenBank accession no. MT766308), respectively. The potential isolate Y4 was found to exhibit adhesion, auto-aggregation, co-aggregation, and weak biofilm activity. It also exhibited a high level of antimicrobial activity and antibiotic susceptibility. The safety of K. flava Y4 isolate, which is proposed to be a probiotic, was evaluated through acute oral toxicity test and biogenic amine production test. Moreover, the preservation potential of isolate Y4 was assessed through application on fruits under different temperatures. Thus, our results confirmed that Kocuria flava Y4 is a prospective probiotic and could also be used for the preservation of fruits.

Co-cultivation of sake yeast and Kocuria isolates from the sake brewing process

Kocuria isolates collected from the sake brewing process have inhabited the Narimasa Sake Brewery in Toyama, Japan. To investigate the effect of these actinobacterial isolates on the growth and metabolism of sake yeast, co-cultivation of sake yeast and Kocuria isolates was performed in a medium containing tryptone, glucose and yeast extract (TGY), and a solution containing koji (steamed rice covered with Aspergillus oryzae) and glucose. In the TGY medium, the ethanol concentration and the number of living cells of each microorganism were measured. In the koji solution, the concentrations of ethanol and organic acids (citric acid, lactic acid and succinic acid) were measured. The results showed that in TGY media, the growth of each Kocuria isolate in the co-culture of the two Kocuria isolates was similar to that in each monoculture. However, the growth of both Kocuria isolates was inhibited in the co-cultures of sake yeast and Kocuria isolates. On the other hand, the growth and ethanol productivity of sake yeast did not differ between its monoculture and co-cultures with Kocuria isolates. In the koji solution, Kocuria isolates TGY1120_3 and TGY1127_2 affected the concentrations of ethanol and lactic acid, respectively. Thus, Kocuria isolates affected the microbial metabolism, but the effects were not identical between the two isolates. This strongly suggests that bacteria inhabiting a sake brewery may influence the flavor and taste of sake products of the brewery.

Genomic information of Kocuria isolates from sake brewing process

Bacteria belonging to the genus Kocuria were identified as bacteria peculiar to a sake brewery in Toyama, Japan. Comparison of the 16S rRNA gene sequences revealed two groups of Kocuria isolates. Among known species, one group was similar to K. koreensis (Kk type), and the other, K. uropygioeca (Ku type). We determined complete genomic DNA sequences from two isolates, TGY1120_3 and TGY1127_2, which belong to types Kk and Ku, respectively. Comparison of these genomic information showed that these isolates differ at the species level with different genomic characters. Isolate TGY1120_3 comprised one chromosome and three plasmids, and the same transposon coding region was located on two loci on the chromosome and one locus on one plasmid, suggesting that the genetic element may be transferred between the chromosome and plasmid. Isolate TGY1127_2 comprised one chromosome and one plasmid. This plasmid encoded an identical transposase coding region, strongly suggesting that the genetic element may be transferred between these different isolates through plasmids. These four plasmids carried a highly similar region, indicating that they share a common ancestor. Thus, these two isolates may form a community and exchange their genetic information during sake brewing.

Great Tit (Parus major) Uropygial Gland Microbiomes and Their Potential Defensive Roles

The uropygial gland (preen gland) of birds plays an important role in maintaining feather integrity and hygiene. Although a few studies have demonstrated potential defensive roles of bacteria residing within these glands, the diversity and functions of the uropygial gland microbiota are largely unknown. Therefore, we investigated the microbiota of great tit (Parus major) uropygial glands through both isolation of bacteria (culture-dependent) and 16S rRNA amplicon sequencing (culture-independent). Co-culture experiments of selected bacterial isolates with four known feather-degrading bacteria (Bacillus licheniformis, Kocuria rhizophila, Pseudomonas monteilii, and Dermacoccus nishinomiyaensis), two non-feather degrading feather bacteria, one common soil bacterial pathogen and two common fungal pathogens enabled us to evaluate the potential antimicrobial properties of these isolates. Our results show major differences between bacterial communities characterized using culture-dependent and -independent approaches. In the former, we were only able to isolate 12 bacterial genera (dominated by members of the Firmicutes and Actinobacteria), while amplicon sequencing identified 110 bacterial genera (dominated by Firmicutes, Bacteroidetes, and Proteobacteria). Uropygial gland bacterial isolates belonging to the genera Bacillus and Kocuria were able to suppress the growth of four of the nine tested antagonists, attesting to potential defensive roles. However, these bacterial genera were infrequent in our MiSeq results suggesting that the isolated bacteria may not be obligate gland symbionts. Furthermore, bacterial functional predictions using 16S rRNA sequences also revealed the ability of uropygial gland bacteria to produce secondary metabolites with antimicrobial properties, such as terpenes. Our findings support that uropygial gland bacteria may play a role in feather health and that bacterial symbionts might act as defensive microbes. Future investigations of these bacterial communities, with targeted approaches (e.g., bacterial isolation and chemical analyses), are thus warranted to improve our understanding of the evolution and function of these host-microbe interactions.

Experimental evidence that symbiotic bacteria produce chemical cues in a songbird

Symbiotic microbes that inhabit animal scent glands can produce volatile compounds used as chemical signals by the host animal. Though several studies have demonstrated correlations between scent gland bacterial community structure and host animal odour profiles, none have systematically demonstrated a causal relationship. In birds, volatile compounds in preen oil secreted by the uropygial gland serve as chemical cues and signals. Here, we tested whether manipulating the uropygial gland microbial community affects chemical profiles in the dark-eyed junco (Junco hyemalis). We found an effect of antibiotic treatment targeting the uropygial gland on both bacterial and volatile profiles. In a second experiment, we cultured bacteria from junco preen oil, and found that all of the cultivars produced at least one volatile compound common in junco preen oil, and that most cultivars produced multiple preen oil volatiles. In both experiments, we identified experimentally generated patterns in specific volatile compounds previously shown to predict junco reproductive success. Together, our data provide experimental support for the hypothesis that symbiotic bacteria produce behaviourally relevant volatile compounds within avian chemical cues and signals.

Birds, feather-degrading bacteria and preen glands: the antimicrobial activity of preen gland secretions from turkeys (Meleagris gallopavo) is amplified by keratinase

The function of uropygial glands (preen glands) has been subject to controversial debates. In this study, we evaluated the antimicrobial potential of preen gland secretions of turkeys (Meleagris gallopavo) against 18 microbial strains by means of diffusion tests, broth microdilutions, checkerboard assays and time-kill curves. Furthermore, we tested the hypothesis that lipids exert direct antimicrobial effects on pathogens. Moreover, we checked for mutualistic relationships between the preen gland bacterium Corynebacterium uropygiale with its hosts. We found that preen gland secretions significantly inhibited the growth of a broad spectrum of bacteria and fungi, particularly when combined with keratinase. Combinations effectively killed multidrug resistant microorganisms in a strongly synergistic manner. Since feather-degrading microorganisms (FDM) express keratinase and thereby disrupt the integrity of the plumage, our data suggests that preen gland secretions of turkeys are specifically activated in the presence of FDM, and specifically eliminate FDM from feathers. However, antimicrobial effects did not originate from lipids, but were mediated by highly polar compounds which might be antimicrobial peptides (AMPs). Finally, C. uropygiale is apparently not involved in the antimicrobial activity of preen gland secretions of turkeys. In conclusion, our results suggest that turkeys can antagonize FDM by amplifying the antimicrobial properties of their preen gland secretions.

Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata)

Avian uropygial glands have received increasing attention in recent years, but little is known about micro-organisms in uropygial glands. In this study, we isolated a strain of Gram-stain-positive, non-motile, non-spore-forming cocci, designated 442^T, from the uropygial gland of an American barn owl (Tyto furcata) and characterized it using a polyphasic approach. 16S rRNA gene sequence analysis placed the isolate in the genus Kocuria. The G+C content was 70.8 mol%, the major menaquinone was MK-7(H2) and the predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Phylogenetic analyses based on the 16S rRNA gene identified Kocuria rhizophila DSM 11926^T (99.6 % similarity), Kocuria salsicia DSM 24776^T (98.7 %), Kocuria varians DSM 20033^T (98.3 %) and Kocuria marina DSM 16420^T (98.3 %) as the most closely related species. However, average nucleotide identity values below 86 % indicated that the isolate differed from all species hitherto described. Chemotaxonomic analyses and whole-cell protein profiles corroborated these findings. Accordingly, the isolate is considered to be a member of a novel species, for which the name Kocuria tytonis sp. nov. is proposed. The type strain is 442^T (=DSM 104130^T=LMG 29944^T).

Kocuria tytonicola, new bacteria from the preen glands of American barn owls (Tyto furcata)

Although birds are hosts to a large number of microorganisms, microbes have rarely been found in avian oil glands. Here, we report on two strains of a new bacterial species from the preen oil of American barn owls (Tyto furcata). Phenotypic as well as genotypic methods placed the isolates to the genus Kocuria. Strains are non-fastidious, non-lipophilic Gram-positive cocci and can be unambiguously discriminated from their closest relative Kocuria rhizophila DSM 11926^T. In phylogenetic trees, the owl bacteria formed a distinct cluster which was clearly separated from all other known Kocuria species. The same conclusion was drawn from MALDI-TOF MS analyses. Once again, the new bacterial strains were very similar to one another, but exhibited substantial differences when compared to the most closely related species. Besides, the results of the biochemical tests, optimum growth conditions and pigmentation differed from closely related Kocuria spp. Finally, ANIb values of less than 87% provided striking evidence that the isolates recovered from American barn owls represent a hitherto undescribed species, for which we propose the name Kocuria tytonicola sp. nov. The type strain is 489^T (DSM 104133^T=LMG 29945^T, taxonumber TA00340).

Corynebacterium heidelbergense sp. nov., isolated from the preen glands of Egyptian geese (Alopochen aegyptiacus)

Two strains (pedersoli^T and girotti) of a new species of bacteria were isolated from the preen glands of wild Egyptian geese (Alopochen aegyptiacus) from the river Neckar in southern Germany in two subsequent years. The strains were lipophilic, fastidious, Gram-positive rods and belonged to the genus Corynebacterium. Phylogenetically, the isolates were most closely related to Corynebacterium falsenii DSM 44353^T which has been found to be associated with birds before. 16S rRNA gene sequence similarity to all known Corynebacterium spp. was significantly <97%. Corresponding values of rpoB showed low levels of similarity <87% and ANIb was <73%. G+C content of the genomic DNA was 65.0mol% for the type strain of the goose isolates, as opposed to 63.2mol% in Corynebacterium falsenii. MALDI-TOF MS analysis of the whole-cell proteins revealed patterns clearly different from the related species, as did biochemical tests, and polar lipid profiles. We therefore conclude that the avian isolates constitute strains of a new species, for which the name Corynebacterium heidelbergense sp. nov. is proposed. The type strain is pedersoli^T (=DSM 104638^T=LMG 30044^T).