The skin microbiome of vertebrates

Composition and diversity of 16S rRNA based skin bacterial microbiome in healthy horses

Characterization of microbiota structure on the skin of healthy horses is important for further development of modulation strategies to ensure optimal bacterial composition for physiological processes. This requirement is also supported by the relatively high incidence of dermatological diseases in horses and thus the need to manage them therapeutically. The taxonomic analysis of skin samples (n = 30) from five different body parts of clinically healthy Shetlands ponies females (neck, back, abdomen, pastern, muzzle) kept under homogeneous conditions (in open stalls with paddock, feed with dry hay, green grass ad libitum and granulated feed) was performed using amplification of V3-V4 region of the 16S rRNA gene. Results indicate that bacteria associated with healthy equine skin represent 18 phyla, 29 classes and 119 families. The most abundant phyla were Proteobacteria (30.8 ± 9.1%) followed by Actinobacteriota (20.4 ± 7.6%), Firmicutes (19.5 ± 10.1%), Bacteroidota (8.5 ± 5.0%) and Deinococcota (7.2 ± 14.8%). Among 229 genera identified, Corynebacterium (7.4 ± 6.5%) was the most abundant genus in skin sites of horses, followed by Deinococcus (7.1 ± 14.9%) and Macrococcus (5.0 ± 8.2%). Indices for the richness and diversity of species within bacterial populations for five regions of horses skin revealed no significant variations observed for species richness (Chao1, p-value 0.2001) but significant result for species evenness (Shannon, p-value 0.0049) with maximum on the neck and minimum on the back skin site. The clustering was seen across samples from different skin sites but also across samples collected from individual horses.

Environmental factors and host sex influence the skin microbiota structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia

Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, poses a significant threat to amphibian biodiversity worldwide. Antifungal bacteria found on the skin of chytrid-resistant amphibians could potentially provide defense against chytridiomycosis and lower mortality rates among resistant individuals. The Hong Kong newt (Paramesotriton hongkongensis) is native to East Asia, a region suspected to be the origin of chytrids, and has exhibited asymptomatic infection, suggesting a long-term coexistence with the chytrids. Therefore, the skin microbiota of this resistant species warrant investigation, along with other factors that can affect the microbiota. Among the 149 newts sampled in their natural habitats in Hong Kong, China, putative antifungal bacteria were found in all individuals. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria; abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiota compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites that could be vital to P. hongkongensis. The dominant cores included the family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiota compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as developing probiotic treatments for susceptible species.

Virulence determinants and antibiotic resistance in staphylococci isolated from the skin of captive bred reptiles

Knowledge of the composition and properties of skin microbiota in healthy reptiles is essential for preservation strategies and thus the prevention of skin dysbiosis leading to dermatological diseases. Despite the greatly increasing popularity of reptiles as pets, only a few studies have dealt with this topic. Therefore, the aim of this work was to analyse species composition of bacteria isolated from skin swabs of 40 reptiles (17 species) using MALDI-TOF spectrometry and to characterise the virulence properties of identified staphylococci (n = 51). The most common species were Staphylococcus xylosus and S. sciuri. Bacilli, enterococci, Escherichia coli, Salmonella sp. and Acinetobacter sp. were also common. The most frequent antimicrobial resistance in staphylococcal isolates was observed for ampicillin (100.0%) and cefoxitin (98.0%) with the blaZ gene being most prevalent (58.8%). In contrast, all staphylococci were susceptible to gentamicin, kanamycin and imipenem. Slime and biofilm production was observed in 86.3% and 76.5% of isolates, respectively. Gelatinase, DNase, protease and lipase activity was found more rarely (41.2%; 25.5%; 27.5% and 21.6%). Since reptiles are a reservoir of bacteria for their owners, common multi-drug resistance (84.3%, MAR index average 0.29 ± 0.09) and biofilm formation must be kept in mind, especially in the case of injury when handling reptiles.

Variable effects of captivity on microbiomes in populations of IUCN-endangered Blanding's turtles (Emydoidea blandingii)

AIMS

Microbiome composition is increasingly considered in species reintroduction efforts and may influence survival and reproductive success. Many turtle species are threatened by anthropogenic pressures and are frequently raised in captivity for reintroduction efforts, yet little is known about turtle microbiome composition in either wild or captive settings. Here, we investigated trends in microbiome composition of captive and wild IUCN-endangered Blanding's turtles (Emydoidea blandingii).

METHODS AND RESULTS

We amplified and sequenced the V4 region of the 16S rDNA locus from plastron, cloaca, and water samples of wild E. blandingii adults and two populations of captive E. blandingii juveniles being raised for headstarting. Plastron, cloaca, and water-associated microbiomes differed strongly from each other and were highly variable among captive sites and between captive and wild sites. Across plastron, cloaca, and water-associated microbial communities, microbial diversity changed over time, but not in a predictable direction between captive sites. Plastron beta diversity correlated with growth rate in captive samples, indicating that external microbiomes may correlate with individual fitness.

CONCLUSIONS

Our results indicate that external and internal microbiomes vary between captive and wild turtles and may reflect differences in fitness of captive-raised individuals.

Baseline Skin Microbiota of the Leatherback Sea Turtle

The integumentary system of the leatherback sea turtle (Dermochelys coriacea) is the most visible and defining difference of the species, with its smooth and waxy carapace and finely scaled skin, distinguishing it from the other six sea turtle species. The skin is the body's largest organ and serves as a primary defense against the outside world and is thus essential to health. To date, we have begun to understand that the microorganisms located on the skin aid in these functions. However, many host-microbial interactions are not yet fully defined or understood. Prior to uncovering these crucial host-microbial interactions, we must first understand the communities of microorganisms present and how they differ through life-stage classes and across the body. Here, we present a comprehensive bacterial microbial profile on the skin of leatherbacks. Using next-generation sequencing (NGS), we identified the major groups of bacteria on the skin of neonates at emergence, neonates at 3-4 weeks of age (i.e., post-hatchlings), and nesting females. These data show that the predominant bacteria on the skin of the leatherback are different at each life-stage class sampled. This suggests that there is a shift in the microbial communities of the skin associated with life-stage class or even possibly age. We also found that different sample locations on the nesting female (i.e., carapace and front appendages = flipper) have significantly different communities of bacteria present. This is likely due to differences in the microhabitats of these anatomic locations and future studies should explore if this variation also holds true for neonates. These data define baseline skin microbiota on the leatherback and can serve as a foundation for additional work to broaden our understanding of the leatherbacks' host-microbial interactions, the impacts of environmental changes or stressors over time, and even the pathogenicity of disease processes.

An insight into the microbiome associated with the damage of raw animal hide and skin-primarily protein, during leather making

Leather processing is vital for the economy of many developing countries, nevertheless, this industry is faced with issues of leather down-grading owing to its low quality leading to economic loss. In addition to defects due to scratch, wound, scar, etc., the down-grading of hide and skin due to microbial putrefaction is also of concern. The major components of raw hide and skin being proteins, fats and minerals, they act as excellent medium for the growth and proliferation of bacteria, leading to putrefaction. Sometimes the damage is more apparent at pickled and wet-blue stage of leather making. The tanned leather is prone to decay by fungi during processing and even after storage as well. Hence, it is quite essential to understand the microbiome of raw hide and skin to gain a deeper insight into the process of putrefaction. This review aims to discuss about the microbes commonly associated with putrefaction of raw animal hide and skin which are capable to cause putrefaction. A few occasions, where infection was caused due to microbes during the life span of animal but the defect was visible only after leather was made out of the hide and skin of infected animal, have also been discussed.

Interactions between microsporidia and other members of the microbiome

The microbiome is the collection of microbes that are associated with a host. Microsporidia are intracellular eukaryotic parasites that can infect most types of animals. In the last decade, there has been much progress to define the relationship between microsporidia and the microbiome. In this review, we cover an increasing number of reports suggesting that microsporidia are common components of the microbiome in both invertebrates and vertebrates. These microsporidia infections can range from mutualistic to pathogenic, causing several physiological phenotypes, including death. Infection with microsporidia often causes a disruption in the normal microbiome, with both increases and decreases of bacterial, fungal, viral, and protozoan species being observed. This impact on the microbiome can occur through upregulation and downregulation of innate immunity as well as morphological changes to tissues that impact interactions with these microbes. Other microbes, particularly bacteria, can inhibit microsporidia and have been exploited to control microsporidia infections. These bacteria can function through regulating immunity, secreting anti-microsporidia compounds, and, in engineered versions, expressing double-stranded RNA targeting microsporidia genes. We end this review by discussing potential future directions to further understand the complex interactions between microsporidia and the other members of the microbiome.

Nonspecific immune, histology and accumulation of marine worm, Urechis unicinctus in response to bisphenol A (BPA)

Bisphenol A (BPA) is one of the environmental endocrine disruptors, due to its chemical stability it exists in abundant concentrations in water and soil consequently accumulating in the food chain and causing many endocrine-related health problems. So far, studies on the effects of BPA on marine invertebrates have focused on acute toxicity, endocrine regulation, reproduction, and development. However, fewer studies have been conducted on marine benthos. The current study aimed to detect the accumulation of BPA and its impact on tissue structure, antioxidant capacity, and immune indexes in marine worm, Urechis unicinctus. U. unicinctus, as a common marine benthic animal, were exposed to different concentrations of BPA. Blood cells and intestinal tract were taken for tissue structure inspection, and supernatant of the coelomic fluid was collected for oxidative and antioxidant biomarkers. Results showed that the accumulation of BPA in muscles of U. unicinctus tended to increase with exposure time. BPA induced a rise in H2O2 and MDA content, and altered the activities of CAT, T-SOD, GST, LSZ and ACP, weaken the immune system functions. Moreover, pathological observation showed that BPA caused severe histopathology in the respiratory intestine, stomach, and midgut. These results will be helpful to understand the response mechanism of U. unicinctus under BPA exposure and provide a reference for controlling the aquaculture conditions and marine water quality of U. unicinctus.

The involvement of Pseudoterranova decipiens fish infestation on the shelf-life of fresh Atlantic cod (Gadus morhua) fillet

Zoonotic nematodes of the family Anisakidae are highly common in many marine fish species, which act as paratenic hosts for the third larval stage. In the fish, these parasites may migrate from the fish's gastro-intestinal tract (GI-tract) further to the coelomic cavity and muscles, making them a possible contamination source of bacteria they carry on their cuticle and in their GI-tract. A previous study revealed no apparent effect of Anisakis simplex on spoilage of fish, but the equally common anisakid species Pseudoterranova decipiens has a larger body surface potentially increasing the bacterial load brought into the fish muscle upon migration. As the presence of shelf-life reducing spoilage bacteria in the microbiome of this anisakid species has been demonstrated, the objective of the present study was to assess the potential shelf-life reducing effect of P. decipiens in fresh fish fillets stored in a domestic refrigerator. Atlantic cod was used as a model since members of the cod family are the third most consumed marine fish globally and it has the highest prevalence of P. decipiens infections. Infected and non-infected codfish fillet portions were collected and microbiologically analyzed at day 0 and day 4 of storage in a domestic fridge. Three isolation media were used to enhance maximum bacterial recovery and isolates were identified using MALDI-TOF MS and 16S rRNA gene sequencing. In parallel to the microbiological examination, sensory analysis was performed daily on the cod fillets to evaluate the freshness of the fish. Results revealed the presence of typical spoilage bacteria (e.g., Pseudomonas sp., Photobacterium sp.) in all fish, but based on the total viable counts, total H2S-producing bacteria, and sensory analysis, there were no objective indications to assume an increased fish spoilage rate by the presence and migration P. decipiens. Additionally, a beta-diversity comparison revealed no significant differences in microbiota composition between infected and non-infected fish parts, though individual heterogeneity in microbiome composition among Atlantic codfish individuals was found. As total viable counts did, however, exceed the guideline limits for fresh fish, further research should now focus on the role of the candling step as a potential source of post-harvest contamination. As such, anisakid infection might still accelerate fish spoilage, though now in an indirect way.

Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats

Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.

Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders

Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.

Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets

Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.

When the host's away, the pathogen will play: the protective role of the skin microbiome during hibernation

The skin of animals is enveloped by a symbiotic microscopic ecosystem known as the microbiome. The host and microbiome exhibit a mutualistic relationship, collectively forming a single evolutionary unit sometimes referred to as a holobiont. Although the holobiome theory highlights the importance of the microbiome, little is known about how the skin microbiome contributes to protecting the host. Existing studies focus on humans or captive animals, but research in wild animals is in its infancy. Specifically, the protective role of the skin microbiome in hibernating animals remains almost entirely overlooked. This is surprising, considering the massive population declines in hibernating North American bats caused by the fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome. Hibernation offers a unique setting in which to study the function of the microbiome because, during torpor, the host's immune system becomes suppressed, making it susceptible to infection. We conducted a systematic review of peer-reviewed literature on the protective role of the skin microbiome in non-human animals. We selected 230 publications that mentioned pathogen inhibition by microbes residing on the skin of the host animal. We found that the majority of studies were conducted in North America and focused on the bacterial microbiome of amphibians infected by the chytrid fungus. Despite mentioning pathogen inhibition by the skin microbiome, only 30.4% of studies experimentally tested the actual antimicrobial activity of symbionts. Additionally, only 7.8% of all publications studied defensive cutaneous symbionts during hibernation. With this review, we want to highlight the knowledge gap surrounding skin microbiome research in hibernating animals. For instance, research looking to mitigate the effects of white-nose syndrome in bats should focus on the antifungal microbiome of Palearctic bats, as they survive exposure to the Pseudogymnoascus destructans -pathogen during hibernation. We also recommend future studies prioritize lesser-known microbial symbionts, such as fungi, and investigate the effects of a combination of anti-pathogen microbes, as both areas of research show promise as probiotic treatments. By incorporating the protective skin microbiome into disease mitigation strategies, conservation efforts can be made more effective.

Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish

Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).

Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome

BACKGROUND

While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation.

RESULTS

We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes.

CONCLUSIONS

Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.

Occurrence and Antimicrobial Resistance among Staphylococci Isolated from the Skin Microbiota of Healthy Goats and Sheep

Staphylococci colonize the skin and mucous membranes of different animals. The purpose of this study was to determine the staphylococcal composition of the skin microbiota of healthy, non-vet visiting, and antimicrobially non-treated sheep and goats. In total, 83 strains (44 from goats and 39 from sheep) were isolated and identified using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). The diversity of the isolated Staphylococcus species was relatively high, and only coagulase-negative staphylococci (CoNS) were isolated. In sheep, S. vitulinus (9/39, 23.1%) was the most common species, followed by S. equorum (8/39, 20.5%), S. lentus (7/39, 17.9%), S. sciuri (6/39, 15.4%), S. xylosus (6/39, 15.4%), S. warneri (1/39, 2.6%), S. simulans (1/39, 2.6%), and S. nepalensis (1/39, 2.6%). In the goats, the most common species was S. sciuri, which was detected in 13 (29.5%) animals. The goat skin was also inhabited by S. equorum (7/44, 15.9%), S. vitulinus (6/44, 13.6%), S. cohnii (5/44, 11.4%), S. lentus (4/44, 9.1%), S. suscinus (3/44, 6.8%), S. caprae, (2/44, 4.5%), S. auricularis (2/44, 4.5%), S. warneri (1/44, 2.3%), and S. xylosus (1/44, 2.3%). Only one S. xylosus strain of goat origin carried the enterotoxin gene (sea). Antimicrobial resistance was not common among the isolated staphylococci. Only 31 (37.3%) strains were resistant to at least one antimicrobial agent, with the highest frequency of resistance to penicillin (16.8%), followed by clindamycin (9.6%), erythromycin (8.4%), moxifloxacin (8.4%), and tetracycline (7.2%). All isolates were susceptible to eight antibiotics (amikacin, gentamycin, ciprofloxacin, levofloxacin, rifampicin, chloramphenicol, trimethoprim-sulfamethoxazole, and tigecycline), representing six different classes. Three isolates displayed a multi-resistance phenotype (MDR): the goat isolates S. cohnii and S. sciuri, as well as the ewe isolate S. xylosus. The MDR S. cohnii isolate was found to be methicillin-resistant and carried the mecA gene. Moreover, the staphylococci isolated from the healthy animals carried genes conferring resistance to β-lactams (mecA, blaZ), tetracyclines (tetL, tetK), macrolides (ermB, ermC), lincosamides (lnu), and fluoroquinolones (grlA). However, the prevalence of these genes was low.

Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns

Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.

Host phylogeny and environment shape the diversity of salamander skin bacterial communities

The composition and diversity of animal-associated microbial communities are shaped by multiple ecological and evolutionary processes acting at different spatial and temporal scales. Skin microbiomes are thought to be strongly influenced by the environment due to the direct interaction of the host's skin with the external media. As expected, the diversity of amphibian skin microbiomes is shaped by climate and host sampling habitats, whereas phylogenetic effects appear to be weak. However, the relative strength of phylogenetic and environmental effects on salamander skin microbiomes remains poorly understood. Here, we analysed sequence data from 1164 adult salamanders of 44 species to characterise and compare the diversity and composition of skin bacteria. We assessed the relative contribution of climate, host sampling habitat, and host phylogeny to the observed patterns of bacterial diversity. We found that bacterial alpha diversity was mainly associated with host sampling habitat and climate, but that bacterial beta diversity was more strongly associated with host taxonomy and phylogeny. This phylogenetic effect predominantly occurred at intermediate levels of host divergence (0-50 Mya). Our results support the importance of environmental factors shaping the diversity of salamander skin microbiota, but also support host phylogenetic history as a major factor shaping these bacterial communities.

Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project

Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.

Ontogeny drives shifts in skin bacterial communities in facultatively paedomorphic salamanders

Microbiomes are major determinants of host growth, development and survival. In amphibians, host-associated bacteria in the skin can inhibit pathogen infection, but many processes can influence the structure and composition of the community. Here we quantified the shifts in skin-associated bacteria across developmental stages in the striped newt (Notophthalmus perstriatus), a threatened salamander species with a complex life history and vulnerable to infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis and ranavirus. Our analyses show that pre-metamorphic larval and paedomorphic stages share similar bacterial compositions, and that the changes in the microbiome coincided with physiological restructuring during metamorphosis. Newts undergoing metamorphosis exhibited microbiome compositions that were intermediate between paedomorphic and post-metamorphic stages, further supporting the idea that metamorphosis is a major driver of host-associated microbes in amphibians. We did not find support for infection-related disruption of the microbiome, though infection replicates were small for each respective life stage.

The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior

Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.

Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques

While skin microbes are known to mediate human health and disease, there has been minimal research on the interactions between skin microbiota, social behavior, and year-to-year effects in non-human primates-important animal models for translational biomedical research. To examine these relationships, we analyzed skin microbes from 78 rhesus macaques living on Cayo Santiago Island, Puerto Rico. We considered age, sex, and social group membership, and characterized social behavior by assessing dominance rank and patterns of grooming as compared to nonsocial behaviors. To measure the effects of a shifting environment, we sampled skin microbiota (based on sequence analysis of the 16S rRNA V4 region) and assessed weather across sampling periods between 2013 and 2015. We hypothesized that, first, monkeys with similar social behavior and/or in the same social group would possess similar skin microbial composition due, in part, to physical contact, and, second, microbial diversity would differ across sampling periods. We found significant phylum-level differences between social groups in the core microbiome as well as an association between total grooming rates and alpha diversity in the complete microbiome, but no association between microbial diversity and measures of rank or other nonsocial behaviors. We also identified alpha and beta diversity differences in microbiota and differential taxa abundance across two sampling periods. Our findings indicate that social dynamics interact with yearly environmental changes to shape the skin microbiota in rhesus macaques, with potential implications for understanding the factors affecting the microbiome in humans, which share many biological and social characteristics with these animals. IMPORTANCE Primate studies are valuable for translational and evolutionary insights into the human microbiome. The majority of primate microbiome studies focus on the gut, so less is known about the factors impacting the microbes on skin and how their links affect health and behavior. Here, we probe the impact of social interactions and the yearly environmental changes on food-provisioned, free-ranging monkeys living on a small island. We expected animals that lived together and groomed each other would have more similar microbes on their skin, but surprisingly found that the external environment was a stronger influence on skin microbiome composition. These findings have implications for our understanding of the human skin microbiome, including potential manipulations to improve health and treat disease.

Biodiversity of Skin Microbiota as an Important Biomarker for Wound Healing

Cutaneous wound healing is a natural and complex repair process that is implicated within four stages. However, microorganisms (e.g., bacteria) can easily penetrate through the skin tissue from the wound bed, which may lead to disbalance in the skin microbiota. Although commensal and pathogenic bacteria are in equilibrium in normal skin, their imbalance in the wound area can cause the delay or impairment of cutaneous wounds. Moreover, skin microbiota is in constant crosstalk with the immune system and epithelial cells, which has significance for the healing of a wound. Therefore, understanding the major bacteria species in the cutaneous wound as well as their communication with the immune system has gained prominence in a way that allows for the emergence of a new perspective for wound healing. In this review, the major bacteria isolated from skin wounds, the role of the crosstalk between the cutaneous microbiome and immune system to heal wounds, the identification techniques of these bacteria populations, and the applied therapies to manipulate the skin microbiota are investigated.

Microbiomes of Blood-Feeding Triatomines in the Context of Their Predatory Relatives and the Environment

The importance of gut microbiomes has become generally recognized in vector biology. This study addresses microbiome signatures in North American Triatoma species of public health significance (vectors of Trypanosoma cruzi) linked to their blood-feeding strategy and the natural habitat. To place the Triatoma-associated microbiomes within a complex evolutionary and ecological context, we sampled sympatric Triatoma populations, related predatory reduviids, unrelated ticks, and environmental material from vertebrate nests where these arthropods reside. Along with five Triatoma species, we have characterized microbiomes of five reduviids (Stenolemoides arizonensis, Ploiaria hirticornis, Zelus longipes, and two Reduvius species), a single soft tick species, Ornithodoros turicata, and environmental microbiomes from selected sites in Arizona, Texas, Florida, and Georgia. The microbiomes of predatory reduviids lack a shared core microbiota. As in triatomines, microbiome dissimilarities among species correlate with dominance of a single bacterial taxon. These include Rickettsia, Lactobacillus, "Candidatus Midichloria," and Zymobacter, which are often accompanied by known symbiotic genera, i.e., Wolbachia, "Candidatus Lariskella," Asaia, Gilliamella, and Burkholderia. We have further identified a compositional convergence of the analyzed microbiomes in regard to the host phylogenetic distance in both blood-feeding and predatory reduviids. While the microbiomes of the two reduviid species from the Emesinae family reflect their close relationship, the microbiomes of all Triatoma species repeatedly form a distinct monophyletic cluster highlighting their phylosymbiosis. Furthermore, based on environmental microbiome profiles and blood meal analysis, we propose three epidemiologically relevant and mutually interrelated bacterial sources for Triatoma microbiomes, i.e., host abiotic environment, host skin microbiome, and pathogens circulating in host blood. IMPORTANCE This study places microbiomes of blood-feeding North American Triatoma vectors (Reduviidae) into a broader evolutionary and ecological context provided by related predatory assassin bugs (Reduviidae), another unrelated vector species (soft tick Ornithodoros turicata), and the environment these arthropods coinhabit. For both vectors, microbiome analyses suggest three interrelated sources of bacteria, i.e., the microbiome of vertebrate nests as their natural habitat, the vertebrate skin microbiome, and the pathobiome circulating in vertebrate blood. Despite an apparent influx of environment-associated bacteria into the arthropod microbiomes, Triatoma microbiomes retain their specificity, forming a distinct cluster that significantly differs from both predatory relatives and ecologically comparable ticks. Similarly, within the related predatory Reduviidae, we found the host phylogenetic distance to underlie microbiome similarities.

Bacterial community analysis identifies Klebsiella pneumoniae as a native symbiotic bacterium in the newborn Protobothrops mucrosquamatus

BACKGROUND

The study of the native microbiome of organisms is crucial. The connection between the native microbiome and the host affects the formation of the innate immune system and the organism's growth. However, the native microbiome of newborn venomous snakes has not been reported. Therefore, we aimed to determine the oral and skin microbiomes of newborn Protobothrops mucrosquamatus.

RESULTS

We performed 16 S full-length sequencing on 14 samples collected from 7 newborn P. mucrosquamatus individuals, specifically targeting their oral and skin microbiomes. In terms of the oral and skin microbiome, the main species were Klebsiella pneumoniae lineages. According to subspecies/species analysis, the proportion from highest to lowest was K. quasipneumoniae subsp. similipneumoniae, K. pneumoniae subsp. pneumoniae, and K. pneumoniae subsp. rhinoscleromatis. These three bacteria accounted for 62.5% and 85% of the skin and oral activity, respectively. The oral microbiome of newborn P. mucrosquamatus did not comprise common bacteria found in snakebite wounds or oral cultures in adult snakes. Therefore, the source of other microbiomes in the oral cavities of adult snakes may be the environment or prey. Functional Annotation of the Prokaryotic Taxa analysis showed that the skin/oral native microbiome metabolism was related to fermentation and human infection owing to the dominance of K. pneumoniae lineages. The characteristics of K. pneumoniae may impact the development of venom in venomous snakes.

CONCLUSION

The results of the native microbiome in the oral cavity and skin of newborn P. mucrosquamatus demonstrated that the habitat environment and prey capture may affect the composition of bacteria in adult snakes. We hypothesized that the native microbiome influences newborn venomous snakes and that K. pneumoniae lineages related to citrate fermentation may play a role in venom growth. However, further verification of this is required.

Staphylococcal species composition in the skin microbiota of domestic pigeons (Columba livia domestica)

Staphylococci are a natural component of the skin microbiota of many organisms, including humans and birds. As opportunistic pathogens, they can cause a variety of infections in humans. The close contact between domestic pigeons and their owners provide an opportunity for exchange of skin-associated bacteria. In this study, 41 healthy racing pigeons were tested. Staphylococci were detected on the skin of each bird (41/41, 100%). Isolates were identified at the species level using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). The diversity of the Staphylococcus species was relatively high and coagulase-negative staphylococci (CoNS) were predominantly isolated. In total, ten different staphylococcal species were identified. S. lentus (19/41, 46.3%) was noted most frequently. The pigeon skin was also inhabited by S. xylosus (6/41, 14.6%), S. equorum (4/41, 9.8%), S. hyicus (3/41, 7.3%), S. intermedius (2/41, 4.9%), S. sciuri (2/41, 4.9%), S. vitulinus (2/41, 4.9%), S. lugdunensis (1/41, 2.4%), S. hominis (1/41, 2.4%), and S. auricularis (1/41, 2.4%). Our results indicate that domestic pigeons may carry pathogens with zoonotic potential. All strains were susceptible to 12 antibiotics (ciprofloxacin, clindamycin chloramphenicol, erythromycin, fosfomycin, gentamicin, levofloxacin, norfloxacin, rifampicin, tobramycin, trimethoprim/sulfamethoxazole, vancomycin) representing 8 different classes. None isolate displayed a multidrug-resistant phenotype. Resistance to tetracycline (6/41, 14.6%) and to penicillin (4/41, 9.7%) was shown. The mecA gene was not detected in the examined strains and no methicillin-resistant staphylococci were found on the skin of the healthy pigeons.

Evaluating cpn60 for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis

Despite being the most widely used phylogenetic marker for amplicon-based profiling of microbial communities, limited phylogenetic resolution of the 16S rRNA gene limits its use for studies of host-microbe co-evolution. In contrast, the cpn60 gene is a universal phylogenetic marker with greater sequence variation capable of species-level resolution. This research compared mammalian skin microbial profiles generated from cpn60 and 16S rRNA gene sequencing approaches, testing for patterns of phylosymbiosis that suggest co-evolutionary host-microbe associations. An ~560 bp fragment of the cpn60 gene was amplified with universal primers and subjected to high-throughput sequencing. Taxonomic classification of cpn60 sequences was completed using a naïve-Bayesian QIIME2 classifier created for this project, trained with an NCBI-supplemented curated cpn60 database (cpnDB_nr). The cpn60 dataset was then compared to published 16S rRNA gene amplicon data. Beta diversity comparisons of microbial community profiles generated with cpn60 and 16S rRNA gene amplicons were not significantly different, based on Procrustes analysis of Bray-Curtis and UniFrac distances. Despite similar relationships among skin microbial profiles, improved phylogenetic resolution provided by the cpn60 gene sequencing permitted observations of phylosymbiosis between microbial community profiles and their mammalian hosts that were not previously observed with 16S rRNA gene profiles. Subsequent investigation of Staphylococcaceae taxa using the cpn60 gene showed increased phylogenetic resolution compared the 16S rRNA gene profiles, revealing potential co-evolutionary host-microbe associations. Overall, our results demonstrate that 16S rRNA and cpn60 marker genes generate comparable microbial community composition patterns while cpn60 better facilitates analyses, such as phylosymbiosis, that require increased phylogenetic resolution.

Sex-dependent effects of mechanical delousing on the skin microbiome of broodstock Atlantic salmon (Salmo salar L.)

Delousing strategies, including mechanical delousing, are typically used to treat Atlantic salmon (Salmo salar) sea lice infestations. In this study, we evaluate the impact of mechanical delousing (Hydrolicer) on the skin bacterial microbiome of broodstock female and male Atlantic salmon. 16S rDNA sequencing of salmon skin microbial communities was performed immediately before delousing, right after delousing and 2 and 13 days post-delousing (dpd). The skin bacterial community of female salmon was more diverse than that of males at the start of the experiment. Overall, hydrolycer caused losses in alpha diversity in females and increases in alpha diversity in males. Hydrolicer also caused rapid shifts in the skin microbial community composition immediately after delicing in a sex-specific manner. There was a decrease in abundance of Proteobacteria and Bacteriodetes in both female and male salmon, whereas Firmicutes and Tenericutes abundances increased. Interestingly, the female community recovered faster, while the male community remained dysbiotic 13 dpd due to expansions in Bacteroidetes (Pseudomonadaceae) and Firmicutes. Our data suggest that female broodstock are more resilient to Hydrolicer treatment due to their more diverse skin microbiota community, and that sex influences the skin microbial community and therefore host health outcomes during common farming manipulations.

Deciphering roles of microbiota in arsenic biotransformation from the earthworm gut and skin

Biotransformation mediated by microbes can affect the biogeochemical cycle of arsenic. However, arsenic biotransformation mediated by earthworm-related microorganisms has not been well explored, especially the role played by earthworm skin microbiota. Herein, we reveal the profiles of arsenic biotransformation genes (ABGs) and elucidate the microbial communities of the earthworm gut, skin, and surrounding soil from five different soil environments in China. The relative abundance of ABGs in the earthworm skin microbiota, which were dominated by genes associated with arsenate reduction and transport, was approximately three times higher than that in the surrounding soil and earthworm gut microbiota. The composition and diversity of earthworm skin microbiota differed significantly from those of the soil and earthworm gut, comprising a core bacterial community with a relative abundance of 96% Firmicutes and a fungal community with relative abundances of 50% Ascomycota and 13% Mucoromycota. In addition, stochastic processes mainly contributed to the microbial community assembly across all samples. Moreover, fungal genera such as Vishniacozyma and Oomyces were important mediators of ABGs involved in the biogeochemical cycle of arsenic. This is the first study to investigate earthworm skin as a reservoir of microbial diversity in arsenic biotransformation. Our findings broaden the current scientific knowledge of the involvement of earthworms in the arsenic biogeochemical cycle.

Recent advances in covalent organic frameworks (COFs) for wound healing and antimicrobial applications

Covalent organic frameworks (COFs) are crystal-like organic structures such as cartography buildings prepared from appropriately pre-designed construction block precursors. Moreover, after the expansion of the first COF in 2005, numerous researchers have been developing different materials for versatile applications such as sensing/imaging, cancer theranostics, drug delivery, tissue engineering, wound healing, and antimicrobials. COFs have harmonious pore size, enduring porosity, thermal stability, and low density. In addition, a wide variety of functional groups could be implanted during their construction to provide desired constituents, including antibodies and enzymes. The reticular organic frameworks comprising porous hybrid materials connected via a covalent bond have been studied for improving wound healing and dressing applications due to their long-standing antibacterial properties. Several COF-based systems have been planned for controlled drug delivery with wound healing purposes, targeting drugs to efficiently inhibit the growth of pathogenic microorganisms at the wound spot. In addition, COFs can be deployed for combinational therapy using photodynamic and photothermal antibacterial therapy along with drug delivery for healing chronic wounds and bacterial infections. Herein, the most recent advancements pertaining to the applications of COF-based systems against bacterial infections and for wound healing are considered, concentrating on challenges and future guidelines.

The Pathogen Aeromonas salmonicida achromogenes Induces Fast Immune and Microbiota Modifications in Rainbow Trout

Environmental stressors can disrupt the relationship between the microbiota and the host and lead to the loss of its functions. Among them, bacterial infection caused by Aeromonas salmonicida, the causative agent of furunculosis, results in high mortality in salmonid aquaculture. Here, rainbow trout were exposed to A. salmonicida achromogenes and its effects on the taxonomic composition and structure of the microbiota was assessed on different epithelia (gills, skin, and caudal fin) at 6 and 72 h post-infection (hpi) using the V1-V3 region of the 16S rRNA sequencing. Moreover, the infection by the pathogen and immune gene responses were evaluated in the head kidney by qPCR. Our results suggested that α-diversity was highly diverse but predominated by a few taxa while β-diversity was affected very early by infection in the gills after 6 h, subsequently affecting the microbiota of the skin and caudal fin. A dysbiosis of the microbiota and an increase in genera known to be opportunistic pathogens (Aeromonas, Pseudomonas) were also identified. Furthermore, an increase in pro-inflammatory cytokines and virulence protein array (vapa) was observed in trout head kidney as soon as 6 hpi and remained elevated until 72 hpi, while the anti-inflammatory genes seemed repressed. This study suggests that the infection by A. salmonicida achromogenes can alter fish microbiota of gills in the few hours post-infection. This result can be useful to develop a non-invasive technique to prevent disease outbreak in aquaculture.

Advanced Skin Antisepsis: Application of UVA-Cleavable Hydroxyethyl Starch Nanocapsules for Improved Eradication of Hair Follicle-Associated Microorganisms

Hair follicles constitute important drug delivery targets for skin antisepsis since they contain ≈25% of the skin microbiome. Nanoparticles are known to penetrate deeply into hair follicles. By massaging the skin, the follicular penetration process is enhanced based on a ratchet effect. Subsequently, an intrafollicular drug release can be initiated by various trigger mechanisms. Here, we present novel ultraviolet A (UVA)-responsive nanocapsules (NCs) with a size between 400 and 600 nm containing hydroxyethyl starch (HES) functionalized by an o-nitrobenzyl linker. A phase transfer into phosphate-buffered saline (PBS) and ethanol was carried out, during which an aggregation of the particles was observed by means of dynamic light scattering (DLS). The highest stabilization for the target medium ethanol as well as UVA-dependent release of ethanol from the HES-NCs was achieved by adding 0.1% betaine monohydrate. Furthermore, sufficient cytocompatibility of the HES-NCs was demonstrated. On ex vivo porcine ear skin, a strong UVA-induced release of the model drug sulforhodamine 101 (SR101) could be demonstrated after application of the NCs in cyclohexane using laser scanning microscopy. In a final experiment, a microbial reduction comparable to that of an ethanol control was demonstrated on ex vivo porcine ear skin using a novel UVA-LED lamp for triggering the release of ethanol from HES-NCs. Our study provides first indications that an advanced skin antisepsis based on the eradication of intrafollicular microorganisms could be achieved by the topical application of UVA-responsive NCs.

Higher white-nose syndrome fungal isolate yields from UV-guided wing biopsies compared with skin swabs and optimal culture media

BACKGROUND

North American bat populations have suffered severe declines over the last decade due to the Pseudogymnoascus destructans fungus infection. The skin disease associated with this causative agent, known as white-nose syndrome (WNS), is specific to bats hibernating in temperate regions. As cultured fungal isolates are required for epidemiological and phylogeographical studies, the purpose of the present work was to compare the efficacy and reliability of different culture approaches based on either skin swabs or wing membrane tissue biopsies for obtaining viable fungal isolates of P. destructans.

RESULTS

In total, we collected and analysed 69 fungal and 65 bacterial skin swabs and 51 wing membrane tissue biopsies from three bat species in the Czech Republic, Poland and the Republic of Armenia. From these, we obtained 12 viable P. destructans culture isolates.

CONCLUSIONS

Our results indicated that the efficacy of cultures based on wing membrane biopsies were significantly higher. Cultivable samples tended to be based on collections from bats with lower body surface temperature and higher counts of UV-visualised lesions. While cultures based on both skin swabs and wing membrane tissue biopsies can be utilised for monitoring and surveillance of P. destructans in bat populations, wing membrane biopsies guided by UV light for skin lesions proved higher efficacy. Interactions between bacteria on the host's skin also appear to play an important role.

The Epibiotic Microbiota of Wild Caribbean Sea Urchin Spines Is Species Specific

Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the coelomic fluid or the gut microbiota. In this study, the epibiota community associated with four wild Caribbean sea urchin species, Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum, was characterized for the first time. Using 57 sea urchin animal samples, we evaluated the influence of animal species, trophic niches, and geographical location on the composition of the epibiotic microbiota. We found significant differences in the bacterial biota among species and trophic niches, but not among geographical locations. L. variegatus exhibited the highest alpha diversity with high dominance of Fusobacteria, Planctomycetes, and Cyanobacteria, whereas T. ventricosus and D. antillarum were dominated by Firmicutes. T. ventricosus inhabiting the seagrass biotope dominated by Thalassia testudinum meadows had mostly Endozoicomonas. In contrast, samples located in the reef (dominated by corals and other reef builders) had a higher abundance of Kistimonas and Photobacterium. Our findings confirm that the epibiotic microbiota is species-specific, but also niche-dependent, revealing the trophic networks emerging from the organic matter being recycled in the seagrass and reef niches. As echinoids are important grazers of benthic communities, their microbiota will likely influence ecosystem processes.

Dynamics of Bacterial Communities on Eggshells and on Nest Materials During Incubation in the Oriental Tit (Parus minor)

Eggshell bacterial communities may affect hatching success and nestling's condition. Nest materials are in direct contact with the eggshells, but the relationships with the eggshell microbiome during incubation have not been fully elucidated. Here, we characterize eggshell and nest material bacterial communities and their changes during incubation in the Oriental Tit (Parus minor). Bacterial communities on the nest material were relatively stable and remained distinct from the eggshell communities and had higher diversity and greater phylogenetic clustering than the eggshell communities from the same nest, resulting in lower phylogenetic turnover rate of nest material microbiome during incubation than expected by chance. While the species diversity of both communities did not change during incubation, we found significantly greater changes in the structure of bacterial communities on the eggshell than on the nest material. However, eggshell microbiome remained distinct from nest material microbiome, suggesting independent dynamics of the two microbiomes during incubation. We detected an increase in the relative abundance of several bacterial taxa on the eggshell that likely come from the bird's skin, feathers, cloaca/intestine, or uropygial secretion which suggests some exchange of bacteria between the incubating bird and the eggshell. Furthermore, incubation appeared to promote the abundance of antibiotic producing taxa on the eggshell, which may hypothetically inhibit growth of many bacteria including pathogenic ones. Our results suggest that the future studies should focus on simultaneous monitoring of absolute abundance as well as relative abundance in communities on eggshells, nest materials, and the incubating bird's body.

External and Internal Microbiomes of Antarctic Nematodes are Distinct, but More Similar to each other than the Surrounding Environment

Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to host physiology. For nematodes, single strains of bacteria are known to adhere to the cuticle (e.g., Pasteuria penetrans), but the structure of a full external microbial community is uncertain. In prior research, we showed that internal gut microbiomes of nematodes (Plectus murrayi, Eudorylaimus antarcticus) and tardigrades from Antarctica's McMurdo Dry Valleys were distinct from the surrounding environment and primarily driven by host identity. Building on this work, we extracted an additional set of individuals containing intact external microbiomes and amplified them for 16S and 18S rRNA metabarcoding. Our results showed that external bacterial microbiomes were more diverse than internal microbiomes, but less diverse than the surrounding environment. Host-specific bacterial compositional patterns were observed, and external microbiomes were most similar to their respective internal microbiomes. However, external microbiomes were more influenced by the environment than the internal microbiomes were. Non-host eukaryotic communities were similar in diversity to internal eukaryotic communities, but exhibited more stochastic patterns of assembly compared to bacterial communities, suggesting the lack of a structured external eukaryotic microbiome. Altogether, we provide evidence that nematode and tardigrade cuticles are inhabited by robust bacterial communities that are substantially influenced by the host, albeit less so than internal microbiomes are.

The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection

BACKGROUND

Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome.

RESULTS

We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity.

CONCLUSIONS

Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).

Micro"bee"ota: Honey Bee Normal Microbiota as a Part of Superorganism

Honey bees are model organisms for microbiota research. Gut microbiomes are very interesting for surveys due to their simple structure and relationship with hive production. Long-term studies reveal the gut microbiota patterns of various hive members, as well as the functions, sources, and interactions of the majority of its bacteria. But the fungal non-pathogenic part of gut microbiota is almost unexplored, likewise some other related microbiota. Honey bees, as superorganisms, interact with their own microorganisms, the microbial communities of food stores, hive surfaces, and other environments. Understanding microbiota diversity, its transition ways, and hive niche colonization control are necessary for understanding any separate microbiota niche because of their interplay. The long coevolution of bees with the microorganisms populating these niches makes these systems co-dependent, integrated, and stable. Interaction with the environment, hive, and other bees determines caste lifestyle as well as individual microbiota. In this article, we bring together studies on the microbiota of the western honey bee. We show a possible relationship between caste determination and microbiota composition. And what is primary: caste differentiation or microbiota composition?

Hematophagy and tick-borne Rickettsial pathogen shape the microbial community structure and predicted functions within the tick vector, Amblyomma maculatum

Background

Ticks are the primary vectors of emerging and resurging pathogens of public health significance worldwide. Analyzing tick bacterial composition, diversity, and functionality across developmental stages and tissues is crucial for designing new strategies to control ticks and prevent tick-borne diseases.

Materials and methods

Here, we explored the microbial communities across the developmental timeline and in different tissues of the Gulf-Coast ticks (Amblyomma maculatum). Using a high-throughput sequencing approach, the influence of blood meal and Rickettsia parkeri, a spotted fever group rickettsiae infection in driving changes in microbiome composition, diversity, and functionality was determined.

Results

This study shows that the core microbiome of Am. maculatum comprises ten core bacterial genera. The genus Rickettsia, Francisella, and Candidatus_Midichloria are the key players, with positive interactions within each developmental stage and adult tick organ tested. Blood meal and Rickettsia parkeri led to an increase in the bacterial abundance in the tissues. According to functional analysis, the increase in bacterial numbers is positively correlated to highly abundant energy metabolism orthologs with blood meal. Correlation analysis identified an increase in OTUs identified as Candidatus Midichloria and a subsequent decrease in Francisella OTUs in Rickettsia parkeri infected tick stages and tissues. Results demonstrate the abundance of Rickettsia and Francisella predominate in the core microbiome of Am. maculatum, whereas Candidatus_Midichloria and Cutibacterium prevalence increase with R. parkeri-infection. Network analysis and functional annotation suggest that R. parkeri interacts positively with Candidatus_Midichloria and negatively with Francisella.

Conclusion

We conclude that tick-transmitted pathogens, such as R. parkeri establishes infection by interacting with the core microbiome of the tick vector.

Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.

Effects of Eucalypt ashes from moderate and high severity wildfires on the skin microbiome of the Iberian frog (Rana iberica)

Forest fires can threaten amphibians because ash-associated contaminants transported by post-fire runoff impact both terrestrial and aquatic ecosystems. Still, the effects of these contaminants on the skin microbiome of amphibians have been overlooked. Thus, the main objective of this study was to assess the effects of ash from different severity wildfires (moderate and high) on the skin microbiome of the Iberian frog (Rana iberica). Bacterial isolates sampled from R. iberica skin microbiome were tested for their antimicrobial activity against the pathogen Aeromonas salmonicida. The isolates with antimicrobial activity were identified and further exposed to several concentrations (0, 6.25, 12.5, 25, 50, 75, and 100%) of Eucalypt (Eucalyptus globulus) aqueous extracts (AAEs) of ash from both a moderate and a high severity wildfire. The results showed that 53% of the bacterial isolates presented antimicrobial activity, with Pseudomonas being the most common genus. Exposure to AAEs had diverse effects on bacterial growth since a decrease, an increase or no effects on growth were observed. For both ash types, increasing AAEs concentrations led to an increase in the number of bacteria whose growth was negatively affected. Ash from the high severity fire showed more adverse effects on bacterial growth than those from moderate severity, likely due to the higher metal concentrations of the former. This study revealed that bacteria living in Iberian frogs' skin could be impaired by ash-related contaminants, potentially weakening the individual's immune system. Given the foreseen increase in wildfires' frequency and severity under climate change, this work raises awareness of the risks faced by amphibian communities in fire-prone regions, emphasising the importance of a rapid implementation of post-fire emergency measures for the preservation and conservation of this group of animals.

Alterations of the Mucosal Immune Response and Microbial Community of the Skin upon Viral Infection in Rainbow Trout (Oncorhynchus mykiss)

The skin is the largest organ on the surface of vertebrates, which not only acts as the first line of defense against pathogens but also harbors diverse symbiotic microorganisms. The complex interaction between skin immunity, pathogens, and commensal bacteria has been extensively studied in mammals. However, little is known regarding the effects of viral infection on the skin immune response and microbial composition in teleost fish. In this study, we exposed rainbow trout (Oncorhynchus mykiss) to infectious hematopoietic necrosis virus (IHNV) by immersion infection. Through pathogen load detection and pathological evaluation, we confirmed that IHNV successfully invaded the rainbow trout, causing severe damage to the epidermis of the skin. qPCR analyses revealed that IHNV invasion significantly upregulated antiviral genes and elicited strong innate immune responses. Transcriptome analyses indicated that IHNV challenge induced strong antiviral responses mediated by pattern recognition receptor (PRR) signaling pathways in the early stage of the infection (4 days post-infection (dpi)), and an extremely strong antibacterial immune response occurred at 14 dpi. Our 16S rRNA sequencing results indicated that the skin microbial community of IHNV-infected fish was significantly richer and more diverse. Particularly, the infected fish exhibited a decrease in Proteobacteria accompanied by an increase in Actinobacteria. Furthermore, IHNV invasion favored the colonization of opportunistic pathogens such as Rhodococcus and Vibrio on the skin, especially in the later stage of infection, leading to dysbiosis. Our findings suggest that IHNV invasion is associated with skin microbiota dysbiosis and could thus lead to secondary bacterial infection.

Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments

Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.

Tracking spoilage bacteria in the tuna microbiome

Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. Yet, many grey areas persist regarding their ecology, conditions of emergence, and proliferation in fish. In this study, we used 16S rRNA barcoding to investigate postmortem changes in the bacteriome of fresh and brine-frozen yellowfin tuna (Thunnus albacares), until late stages of decomposition (i.e. 120 h). The results revealed that despite standard refrigeration storage conditions (i.e. 4°C), a diverse and complex spoilage bacteriome developed in the gut and liver. The relative abundance of spoilage bacterial taxa increased rapidly in both organs, representing 82% of the bacterial communities in fresh yellowfin tuna, and less than 30% in brine-frozen tuna. Photobacterium was identified as one of the dominant bacterial genera, and its temporal dynamics were positively correlated with histamine concentration in both gut and liver samples, which ultimately exceeded the recommended sanitary threshold of 50 ppm in edible parts of tuna. The results from this study show that the sanitary risks associated with the consumption of this widely eaten fish are strongly influenced by postcapture storage conditions.

What lives on and in the sea turtle? A literature review of sea turtle bacterial microbiota

Within the United States, all populations of sea turtles are listed as threatened or endangered under the Endangered Species Act. Identifying methods of supporting health, preventing disease, and treating disease is essential for conservation and management strategies for all species. Over the last few decades, advances in technology and high throughput sequencing have allowed a proliferation of research into core microbiota and microbiomes in humans and animals. Such investigations have proven that microbiota on and within a host can influence physiology, immunity, and development. Accordingly, a comprehensive understanding of microbiota is essential for unearthing the complex relationships within a microbiome and how those interactions and relationships can be used to promote health and prevent or treat disease. The goal of this review is to summarize the current microbiota research available across all species of sea turtles and identify any emerging trends. Methodological differences made it challenging to draw conclusions across studies, but it is apparent that each anatomical location investigated has a unique core microbiota with some potential overlap. In the future, unifying methodology across microbiota studies will allow broader conclusions to be drawn across all anatomic locations and species of sea turtles. These conclusions will then allow clinicians and conservationists to apply the research results in the field. Additionally, future efforts should include a wider range of organisms including fungi, viruses, parasites, epibiota, and archaea to unveil essential relationships among and between the organisms and host for maintenance of a healthy microbiome.

Fishing for the Microbiome of Tropical Tuna

Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.

Short-term continuous and pulse Pb exposure causes negative effects on skin histomorphological structure and bacterial composition of adult Pelophylax nigromaculatus

Lead (Pb) is a toxic heavy metal often present in the environment as a pulse in water. Traditional toxicity tests are usually carried out under conditions of continuous concentration, without considering the impact of pulse exposure on aquatic organisms. This study aimed to evaluate the effects of short-term continuous and pulse Pb exposures on the skin bacteria and histomorphological structure of Pelophylax nigromaculatus. Results showed that compared to the control (CON) and Pb continuous exposure group (CEPb), the Pb pulse exposure group (PEPb) showed the smallest size of granular glands, which would interfere with the permeability and secretory function of skin, making the individual more sensitive to external pollution. Lead exposure significantly changed the composition and diversity of skin bacteria. Compared to the CON and CEPb groups, the PEPb group showed a significant increase in the abundance of harmful bacteria (e.g., Bacteroidetes and Chryseobacterium) and a decrease in the abundance of beneficial bacteria (e.g., Pseudomonas). PICRUSt software showed that there were differences in the metabolic pathway of skin bacteria among the three groups (CON, CEPb, and PEPb). Overall, this study indicates that Pb pulse exposure can aggravate the toxicity of Pb for frog skin, providing a new framework for simulating short-term heavy metal exposure in the context of frog health.

Surface microbiota of Mediterranean loggerhead sea turtles unraveled by 16S and 18S amplicon sequencing

The loggerhead sea turtle is considered a keystone species with a major ecological role in Mediterranean marine environment. As is the case with other wild reptiles, their outer microbiome is rarely studied. Although there are several studies on sea turtle’s macro-epibionts and endo-microbiota, there has been little research on epibiotic microbiota associated with turtle skin and carapace. Therefore we aimed to provide the identification of combined epibiotic eukaryotic, bacterial and archaeal microbiota on Mediterranean loggerhead sea turtles. In this study, we sampled skins and carapaces of 26 loggerheads from the Mediterranean Sea during 2018 and 2019. To investigate the overall microbial diversity and composition, amplicon sequencing of 16S and 18S rRNA genes was performed. We found that the Mediterranean loggerhead sea turtle epibiotic microbiota is a reservoir of a vast variety of microbial species. Microbial communities mostly varied by different locations and seas, while within bacterial communities’ significant difference was observed between sampled body sites (carapace vs. skin). In terms of relative abundance, Proteobacteria and Bacteroidota were the most represented phyla within prokaryotes, while Alveolata and Stramenopiles thrived among eukaryotes. This study, besides providing a first survey of microbial eukaryotes on loggerheads via metabarcoding, identifies fine differences within both bacterial and eukaryotic microbial communities that seem to reflect the host anatomy and habitat. Multi-domain epi-microbiome surveys provide additional layers of information that are complementary with previous morphological studies and enable better understanding of the biology and ecology of these vulnerable marine reptiles.

Microbiome assembly on Drosophila body surfaces benefits the flies to combat fungal infections

In contrast to the well-characterized gut microbiomes, the composition and function of the insect body-surface microbiotas are still elusive and highly underexplored. Here we report the dynamic features of the Drosophila melanogaster surface microbiomes. It was found that the microbiomes assembled on fly surfaces could defend insects against fungal parasitic infections. The substantial increase of bacterial loads occurred within 10 days of fly eclosion, especially the expansion of Gilliamella species. The culturable bacteria such as Lactiplantibacillus plantarum could effectively inhibit fungal spore germinations, and the gnotobiotic addition of the isolated bacteria could substantially delay fungal infection of axenic flies. We found that the fly tarsal segments were largely accumulated with bacterial cells, which could accelerate cell dispersal onto different body parts to deter fungal spore germinations. Our findings will facilitate future investigations of the surface microbiotas affecting insect physiologies.

•

Bacterial loads quickly increase on the body surface of fruit fly after eclosion

•

Surface bacteria can defend flies against fungal parasitic infections

•

Surface bacteria can inhibit fungal spore germinations

•

Expansion of the γ-Proteobacteria Gilliamella on fly surfaces

Factors Influencing Bacterial and Fungal Skin Communities of Montane Salamanders of Central Mexico

Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.