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Animals live in a bacterial world, and detecting and exploring adaptations favouring mutualistic relationships with antibiotic‐producing bacteria as a strategy to fight pathogens are of prime importance for evolutionary ecologists. Uropygial secretion of European hoopoes (Upupa epops, Linnaeus) contains antimicrobials from mutualistic bacteria that may be used to prevent embryo infection. Here, we investigated the microscopic structure of hoopoe eggshells looking for special features favouring the adhesion of antimicrobial uropygial secretions. We impeded female access to the uropygial gland and compared microscopic characteristics of eggshells, bacterial loads of eggs and of uropygial secretion, and hatching success of experimental and control females. Then, we explored the link between microbiological characteristics of uropygial secretion and these of eggs of hoopoes, as well as possible fitness benefits. The microscopic study revealed special structures in hoopoes' eggshells (crypts). The experimental prevention of females' gland access demonstrated that crypts are filled with uropygial secretion and that symbiotic enterococci bacteria on the eggshells come, at least partially, from those in the female's uropygial gland. Moreover, the experiment resulted in a higher permeability of eggshells by several groups of bacteria and in elimination of the positive relationships detected for control nests between hatching success and density of symbiotic bacteria, either in the uropygial secretion of females or on the eggshell. The findings of specialized crypts on the eggshells of hoopoes, and of video‐recorded females smearing secretion containing symbiotic bacteria at a high density onto the eggshells strongly support a link between secretion and bacteria on eggs. Moreover, the detected associations between bacteria and hatching success suggest that crypts enhancing the adhesion of symbiont‐carrying uropygial secretion likely protect embryos against infections.

Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies. This approach shows both coordinated population expansions that demarcate community boundaries and high frequency of positive and negative associations among populations within communities. Our analysis thus highlights that the environmental variability of the coastal ocean is mirrored in sharp transitions of defined but ephemeral communities of organisms. Whether marine microbes form strongly differentiated communities over time remains unknown. Here, Martin-Platero and colleagues develop a time series analysis to characterize marine bacteria and Eukarya communities at a fine temporal grain, revealing cohesive but rapidly changing communities.

1. It has been recently showed that one bacterial strain isolated from the uropygial gland of a nestling hoopoe Upupa epops produced antimicrobial peptides active against a broad spectrum of pathogenic bacteria. These bacteria might thus mediate antimicrobial properties of the uropygial secretions as a consequence of the symbiotic association with hoopoes. 2. We study antimicrobial properties of white (from males and non-breeding females) and brown (from nestlings and breeding females) uropygial gland secretions of hoopoes Upupa epops, as well as the association with the presence of bacteria living inside their uropygial gland. 3. We found that brown, but not white secretions contained bacteria and showed antimicrobial activity against the feather degrading bacterium Bacillus licheniformis. The antagonistic activity of bacterial colonies was mediated by antimicrobial peptides because protease inhibited antimicrobial properties. 4. All except one identified bacterium in aerobic cultures were of the genus Enterococcus, and the microscopic study of uropygial secretions and glands confirmed a high density of bacteria within the gland. 5. Furthermore, we studied potential benefits of antimicrobial peptides produced by symbiotic bacteria of hoopoes by adding protease to incubating nests. 6. The experiment increased bacterial growth and hatching failures in hoopoes but not in spotless starlings Sturnus unicolor, a species that does not harbour bacteria in its uropygial gland. 7. Thus, microbiological, anatomical and ecological results suggest a tight symbiotic interaction between bacteria that produce antibiotic substances and the hoopoes.

Abstract The recent boom in phage therapy and phage biocontrol requires the design of suitable cocktails of genetically different bacteriophages. The current methods for typing phages need significant quantities of purified DNA, may require a priori genetic information and are cost and time consuming. We have evaluated the randomly amplified polymorphic DNA (RAPD)-PCR technique to produce unique and reproducible band patterns from 26 different bacteriophages infecting Staphylococcus epidermidis, Staphylococcus aureus, Lactococcus lactis, Escherichia coli, Streptococcus thermophilus, Bacillus subtilis and Lactobacillus casei bacterial strains. Initially, purified DNA and phage suspensions of seven selected phages were used as a template. The conditions that were found to be optimal 8μM of 10-mer primers, 3μM magnesium oxalacetate and 5% dimethyl sulfoxide. The RAPD genomic fingerprints using a phage titer suspension higher than 109PFUmL−1 were highly reproducible. Clustering by the Pearson correlation coefficient and the unweighted pair group method with arithmetic averages clustering algorithm correlated largely with genetically different phages infecting the same bacterial species, although closely related phages with a similar DNA restriction pattern were indistinguishable. The results support the use of RAPD-PCR for quick typing of phage isolates and preliminary assessment of their genetic diversity bypassing tedious DNA purification protocols and previous knowledge of their sequence.

Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese’s flavor. They form communities that play a crucial role in determining the cheese’s organoleptic properties. The composition of cheeses’ microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.

The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that can cause diverse health care-associated infections. Their genome plasticity enables easy acquisition of virulence factors as well as antibiotic resistances. Urinary tract infections (UTIs) and catheter-associated UTIs are common diseases caused by enterococci. In this study, Enterococcus strains isolated from UTIs were characterized, showing that the majority were E. faecalis and contained several virulence factors associated to a better colonization of the urinary tract. Their susceptibility against the bacteriocin AS-48 and several antibiotics was tested. AS-48 is a potent circular bacteriocin that causes bacterial death by pore formation in the cell membrane. The interest of this bacteriocin is based on the potent inhibitory activity, the high stability against environmental conditions, and the low toxicity. AS-48 was active at concentrations below 10 mg/L even against antibiotic-resistant strains, whereas these strains showed resistance to, at least, seven of the 20 antibiotics tested. Moreover, the effect of AS-48 combined with antibiotics commonly used to treat UTIs was largely synergistic (with up to 100-fold MIC reduction) and only occasionally additive. These data suggest AS-48 as a potential novel drug to deal with or prevent enterococcal infections.

Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host.

Background Animal bacterial symbionts are established early in life, either through vertical transmission and/or by horizontal transmission from both the physical and the social environment, such as direct contact with con- or heterospecifics. The social environment particularly can influence the acquisition of both mutualistic and pathogenic bacteria, with consequences for the stability of symbiotic communities. However, segregating the effects of the shared physical environment from those of the social interactions is challenging, limiting our current knowledge on the role of the social environment in structuring bacterial communities in wild animals. Here, we take advantage of the avian brood-parasite system of Eurasian magpies ( Pica pica ) and great spotted cuckoos ( Clamator glandarius ) to explore how the interspecific social environment (magpie nestlings developing with or without heterospecifics) affects bacterial communities on uropygial gland skin. Results We demonstrated interspecific differences in bacterial community compositions in members of the two species when growing up in monospecific nests. However, the bacterial community of magpies in heterospecific nests was richer, more diverse, and more similar to their cuckoo nest-mates than when growing up in monospecific nests. These patterns were alike for the subset of microbes that could be considered core, but when looking at the subset of potentially pathogenic bacterial genera, cuckoo presence reduced the relative abundance of potentially pathogenic bacterial genera on magpies. Conclusions Our findings highlight the role of social interactions in shaping the assembly of the avian skin bacterial communities during the nestling period, as exemplified in a brood parasite—host system.

Background Animals rely on symbiotic bacteria living within/on their tissues for multiple functions, while simultaneously needing to protect themselves via immune functions or other defenses from potentially pathogenic microorganisms that could invade those tissues. As a result, interactions with complex assemblages of bacteria have driven the evolution of host strategies to control established symbioses. One such strategy involves the development of organs specialized in maintaining associations with beneficial members of the microbial community — so-called symbiotic organs. These organs are characterized by compartmentalizing spaces where favorable conditions for the beneficial bacteria are promoted, while preventing colonization of other tissues. Although several model systems of symbiotic organs have been studied in animals, none have been recognized in non-aquatic vertebrates except for the intestinal crypts of mammals. Here, we propose that bird´s uropygial glands may be specialized symbiotic organs. Results We tested this hypothesis using the uropygial gland of the hoopoe ( Upupa epops ) as a model, which hosts a complex bacterial community that includes antimicrobial-producing symbionts. First, we examined whether the uropygial gland supports a specific symbiotic community, by comparing the microbiome composition of the uropygial secretions and eggshell surfaces in two European hoopoe populations. Additionally, using histological staining and fluorescence in situ hybridization, we looked for structural specializations for compartmentalization and bacterial targeting in the glands of nesting hoopoes in comparison to non-breeding individuals lacking the symbiosis. Results show that, in comparison with bacterial communities of the eggshells, those of the uropygial gland were more conserved between both populations. Moreover, uropygial glands of nesting hoopoes were strictly compartmentalized by a special tissue, properties that are absent in the non-breeding individuals lacking the symbiosis. Finally, bacteria were organized within the organ, suggesting the existence of special physical niches to promote specialized mutualistic symbionts. Conclusions All evidence supports that the hoopoe uropygial gland is a specialized symbiotic organ for bacterial cultivation, paving the way for new insights into vertebrates’ exocrine glands’ role in microbial symbiosis. Clinical trial number Not applicable.

1. The use of feathers as nest lining material has traditionally been explained by the thermoregulatory properties of feathers. Feather nest lining could additionally affect nest detectability by predators, or play a role in a sexually selected context. Furthermore, feather nest lining harbours microorganisms that may influence environmental conditions where eggs and nestlings develop. 2. Microorganisms growing on nest lining feathers could affect the bacterial load of eggshells because they occupy space and/or produce antimicrobial substances against other bacteria, including egg pathogens. Feathers of different colours are known to differ in their bacterial community (i.e. feather degrading bacteria) and, thus, colour composition of nest lining feather could also affect the bacterial environment of avian nests. 3. Here we tested this hypothesis in the barn shallow (Hirundo rustica) by exploring the relationship between eggshell bacterial loads and number of feathers, and the effect of experimentally modified colour composition of nest lining feathers on eggshell bacterial load. 4. In agreement with the hypothesis we found that, before treatment, the number of nest lining feathers (mainly that of unpigmented-white colour) predicted eggshell bacterial load, and that, at the end of the incubation period, eggshells of experimental nests with white feathers had a lower bacterial density than those in experimental nests with black feathers. 5. We failed to detect a relationship between bacterial load and hatching success. However, since evidence of that relationship exists for other species, these results would explain the previously detected experimental effect of colour composition of nest lining feathers on hatching success of swallows. 6. Nest design in general, and the use of nest-lining white feathers in particular, may therefore have important consequences for reproductive success of birds. The reduced eggshell bacterial loads of experimental white nests would explain preferences by barn swallows for feathers of white colour.