The microbiome of bat guano: for what is this knowledge important?

Diversity pattern and antibiotic activity of microbial communities inhabiting a karst cave from Costa Rica

The studies of cave bacterial communities worldwide have revealed their potential to produce antibiotic molecules. In Costa Rica, ~400 caves have been identified; however, their microbial diversity and biotechnological potential remain unexplored. In this work, we studied the chemical composition and microbial diversity of a Costa Rican cave (known as the Amblipigida cave) located in Puntarenas, Costa Rica. Additionally, through culture-dependent methods, we evaluated the potential of its microbiota to produce antibiotic molecules. Mineralogical and elemental analyses revealed that the Amblipigida cave is primarily composed of calcite. However, small variations in chemical composition were observed as a result of specific conditions, such as light flashes or the input of organic matter. The 16S rRNA gene metabarcoding revealed an extraordinarily high microbial diversity (with an average Shannon index of ~6.5), primarily comprising bacteria from the phyla Pseudomonadota, Actinomycetota, Firmicutes and Acidobacteriota, with the family Pseudomonadaceae being the most abundant. A total of 93 bacteria were isolated, of which 15% exhibited antibiotic activity against at least one Gram-positive or yeast strain and were classified within the genera Lysobacter, Streptomyces, Pseudomonas, Brevundimonas and Bacillus. These findings underscore the highly diverse nature of cave microbiota and their significant biotechnological potential, particularly in the production of antibiotic compounds.

Invertebrate composting quality of the invasive alga Rugulopteryx okamurae, prospects for its bio-recycling, management and circular economy

In recent decades, the invasive seaweed Rugulopteryx okamurae has had a huge environmental impact on marine biodiversity, fisheries, GHG emissions and public health along much of the Iberian Peninsula and islands coastline. Due to the enormous amount of algae biomass that is expelled to the beaches where it slowly rots, some circular economy business initiatives, such as composting, are emerging. In the present study, we compared the quality of compost obtained from earthworms (Dendrobaena veneta), cockroaches (Eublaberus sp.), mealworms (Tenebrio molitor) and black soldier fly larvae (Hermetia illucens). Batches fed with 100% organic kitchen waste (control group) were compared with batches fed with 50% algae and 50% kitchen waste (treatment group). Our results show that the most sensitive species (D. veneta and T. molitor) to R. okamurae toxins compost adequately. The C/N ratio, electrical conductivity (EC), pH, total organic matter (TOM), C, K, K2O, Mg, MgO, N, P, P2O5, B, Cu, Ni and Zn of the compost obtained were determined. A high quality compost was obtained in which only the EC values are slightly elevated. Particularly good was the compost obtained with H. illucens and Eublaberus sp. This quality is in agreement with previous research on the mass balance of composting. Therefore, both species offer, in the field of circular economy, encouraging prospects for the development of composting enterprises.

Fungal and bat diversities along a landscape gradient in central Mexico

Species interactions between bats and fungi are poorly known. We documented the association between fungal and bat diversities along a landscape gradient. Ten, eight, and seven bat species were captured in conserved, semi-conserved, and urban sites, respectively. Eptesicus fuscus, Myotis ciliolabrum and Corynorhinus townsendii were the most abundant in conserved and semi-conserved sites. E. fuscus, Myotis velifer, and Lasiurus cinereus were abundant in urban sites. C. townsendii was the least abundant bat. A total of 15 cultivated fungi genera included the fungal diversity in bats, of which nine fungi genera were shared along the landscape gradient. Penicillium and Aspergillus were the most abundant genera, and Aureobasidium, Bispora, Stachybotrys, and Verticillium were only documented in the conserved sites. We observed a higher fungal diversity associated with bat species along this landscape gradient. The individual site-based accumulation curves of fungal diversity showed significant decreasing values along the conserved, semi-conserved, and urban sites, respectively. In conserved and urban sites, M. californicus and M. velifer showed the highest fungal diversity, respectively. E. fuscus was associated to the fungi genera Scopulariopsis, Alternaria, Penicillium and Beauveria; L. cinereus to Cladosporium and Aspergillus, and M. velifer to Alternaria sp1, Bispora and Trichoderma. Conserved sites showed both high bat and fungal diversities [species richness and abundance] compared to semi-conserved and urban sites. More studies associating bat and fungal diversities in other ecosystems are needed to corroborate this pattern.

Gypsum Cave Biofilm Communities are Strongly Influenced by Bat- And Arthropod-Related Fungi

The Gypsum Karst of Sorbas, Almeria, southeast Spain, includes a few caves whose entrances are open and allow the entry and roosting of numerous bats. Caves are characterized by their diversity of gypsum speleothems, such as stalactites, coralloids, gypsum crusts, etc. Colored biofilms can be observed on the walls of most caves, among which the Covadura and C3 caves were studied. The objective was to determine the influence that bat mycobiomes may have on the fungal communities of biofilms. The results indicate that the fungi retrieved from white and yellow biofilms in Covadura Cave (Ascomycota, Mortierellomycota, Basidiomycota) showed a wide diversity, depending on their location, and were highly influenced by the bat population, the guano and the arthropods that thrive in the guano, while C3 Cave was more strongly influenced by soil- and arthropod-related fungi (Ascomycota, Mortierellomycota), due to the absence of roosting bats.

Tick-borne viruses and their risk to public health in the Caribbean: Spotlight on bats as reservoirs in Cuba

In recent decades, tick-borne diseases (TBDs) have surged and expanded globally due to factors like changes in human activities, land use patterns, and climate change, and it have been associated with the emergence of zoonotic diseases. Cuba faces the impact of ticks on human health and the economy. Although Cuba has studied TBDs extensively for the past 50 years, focus on tick-borne viral pathogens affecting humans remains scant. Despite TBDs not currently being a major health concern in Cuba, factors like inadequate clinician awareness, climate conditions, global tick emergence, and evidence of zoonotic pathogens in ticks underscore the importance of enhanced TBD surveillance in the country. Here we revised the available information on ticks as vectors of pathogenic viruses to humans, spotlighting bats as potential reservoirs of tick-borne viruses (TBVs). Ticks on bats have gained interest as potential reservoirs of pathogenic viruses to humans in Cuba and worldwide. Understanding their role in maintaining viruses and their potential transmission to humans is crucial for the implementation of surveillance and control programs to reduce the risk of tick-borne viral diseases and public health management.

Immunoinformatic-guided designing and evaluating protein and mRNA-based vaccines against Cryptococcus neoformans for immunocompromised patients

BACKGROUND

Cryptococcus neoformans is a fungal pathogen that can cause serious meningoencephalitis in individuals with compromised immune systems due to HIV/AIDS (human immunodeficiency virus/acquired immunodeficiency syndrome), liver cirrhosis, and transplantation. Mannoproteins (MPs), glycoproteins in the C. neoformans capsule, crucially impact virulence by mediating adhesion to lung cells and modulating immune response via cytokine induction and phagocytosis influence. Therefore, creating a vaccine that can generate targeted antibodies to fight infection and prevent fungal illnesses is essential.

RESULTS

This research aims to create a unique, stable, and safe vaccine through bioinformatics methodologies, aiming at epitopes of T and B cells found in the MP of C. neoformans. Based on toxicity, immunogenicity, and antigenicity, this research predicted novel T cells (GNPVGGNVT, NPVGGNVTT, QTSYARLLS, TSVGNGIAS, WVMPGDYTN, AAATGSSSSGSTGSG, GSTGSGSGSAAAGST, SGSTGSGSGSAAAGS, SSGSTGSGSGSAAAG, and SSSGSTGSGSGSAAA) and B cell (ANGSTSTFQQRYTGTYTNGDGSLGTWTQGETVTPQTAYSTPATSNCKTYTSVGNGIASLALSNAGSNSTAAATNSSSGGASAAATGSSSSGSTGSGSGSAAAGSTAAASSSGDSSSSTSAAMSNGI, HGATGLGNPVGGNVTT, TMGPTNPSEPTLGTAI, GNPVGGNVTTNATGSD, and NSTAAATNSSSGGASA) epitopes for a multiple-epitope vaccine and constructed a vaccine subunit with potential immunogenic properties. The present study used four linkers (AAY, GPGPG, KK, and EAAAK linkers) to connect the epitopes and adjuvant. After constructing the vaccine, it was confronted with receptor docking and simulation analysis. Subsequently, the vaccine was cloned into the vector of Escherichia coli pET-28a ( +) by ligation process for the expression using the SnapGene tool, which confirmed a significant immune response. To assess the constructed vaccine's properties, multiple computational tools were employed. Based on the MP sequence, the tools evaluated the antigenicity, immunogenicity, cytokine-inducing capacity, allergenicity, toxicity, population coverage, and solubility.

CONCLUSION

Eventually, the results revealed a promising multi-epitope vaccine as a potential candidate for addressing global C. neoformans infection, particularly in immunocompromised patients. Yet, additional in vitro and in vivo investigations are necessary to validate its safety and effectiveness.

Characterization of the bacterial microbiome of non-hematophagous bats and associated ectoparasites from Brazil

Introduction

Bats, along with their ectoparasites, harbor a wide diversity of symbiotic and potential pathogenic bacteria. Despite the enormous diversity of bats (181 species), few studies aimed to investigate the bacterial microbiome of Brazilian chiropterans and associated ectoparasites. This study aimed to characterize the bacterial microbiome of non-hematophagous bats and associated Streblidae flies and Macronyssidae and Spinturnicidae mites in the state of Mato Grosso do Sul, midwestern Brazil.

Methods

Oral and rectal swabs were collected from 30 bats (Artibeus lituratus [n = 13], Artibeus planirostris [n  =  9], Eptesicus furinalis [n = 5], Carollia perspicillata [n = 2], and Platyrrhinus lineatus [n = 1]). In addition, a total of 58 mites (15 Macronyssidae and 43 Spinturnicidae) and 48 Streblidae bat flies were collected from the captured bats. After DNA extraction and purification, each sample's bacterial composition was analyzed with metagenomic sequencing.

Results

The microbiome composition of both oral and rectal bat swab samples showed that Gammaproteobacteria was the most abundant bacterial class. Spiroplasma, Wolbachia and Bartonella represented the most abundant genera in Streblidae flies. While Wolbachia (Alphaproteobacteria) was the most abundant genus found in Spinturnicidae, Arsenophonus (Gammaproteobacteria) was found in high abundance in Macronyssidae mites. In addition to characterizing the microbiome of each sample at the class and genus taxonomic levels, we identified medically significant bacteria able to infect both animals and humans in oral (Streptococcus and Anaplasma) and rectal swabs (Enterobacter, Klebsiella, Escherichia, Enterococcus, Streptococcus), Macronyssidae (Anaplasma, Bartonella, Ehrlichia) and Spinturnicidae (Anaplasma, Bartonella) mites as well as Streblidae flies (Spiroplasma, Bartonella).

Discussion and conclusion

Besides expanding the knowledge on the bacterial microbiome of non-hematophagous bats and Streblidae flies from Brazil, the present work showed, for the first time, the bacterial community of bat-associated Macronyssidae and Spinturnicidae mites.

Speleomycology of Air in Stopića Cave (Serbia)

Fungi can colonize organic matter present in subterranean sites and have a significant role as dwellers in different microniches of cave habitats. In order to analyze the content of airborne fungal propagules in different parts of "Stopića Cave," a touristic site in Serbia, air sampling was carried out in three seasons during 2020, prior to and during the onset of COVID-19 pandemic. Culturable mycobiota was identified using both microscopic techniques and ITS region/BenA gene barcoding, while multivariate analyses were employed to establish the link between fungal taxa and different environmental factors. The maximal measured fungal propagule concentrations were recorded during spring sampling which were based on fungal propagule concentration categories; the cave environment matches the category V. A total of 29 fungal isolates were identified, while Aspergillus, Cladosporium, Fusarium, Lecanicillium, Mucor, and Penicillium were the most diverse genera. According to the trophic mode, most of the isolated fungal species were pathotrophs (75.86%), but when regarding ecological guilds, the most dominant were undefined saprobes and animal pathogens (41.38% for each). Show caves are especially vulnerable to human impacts, and the fungal propagules' concentration within the caves could be good indices for the level of ecological disturbance.

Geochemistry and 14C dating of guano deposits in the Karaftu Cave, Kurdistan, Iran: implication for paleoenvironment

Karaftu Cave in the northwest of Divandareh includes four floors plus an underground area. The bat hall and its underground area are covered with guano deposits. 14C dating indicates the onset of guano deposition is about 14,260±50 BP years, and its average accumulation rate is about 4.1 mm/yr for depths of 360 to 205 cm. Bacterial and fungal metabolisms decay guano, release acids, and disperse large amounts of microorganisms inside the cave. Interactions between acids and guano caused leaching, dissolution, change in the distribution, and abundance of elements, which leads to the formation of secondary minerals in guano. These variations in minerals and elements also depend on the local climatic conditions. Distribution of elements in the Ce/Ce* versus Pr/Pr* diagram and the correlation coefficient between Ce and Mn display three different paleoclimate conditions (dry, wet, and dry) during the accumulation of the guano. Also, dolomite, phosphate, and iron oxide minerals have been formed during the passage of water through bedrock beneath the guano. This water is unsuitable for drinking and harmful to the organisms in the region. Effect of these acids on the substrate also leads to the collapse of the cave floor, generation of a new underground, fall in the groundwater level, change in the groundwater drainage system, drying of springs around the cave, loss of green cover, and a negative impact on the ecosystem in the region. To keep the cave environment clean and remove these problems, it is better to harvest guano and use it as fertilizer.

Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka

Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.

Assessing the threat of bat-associated fungal pathogens

Fungal pathogens have become an increasingly important topic in recent decades. Yet whilst various cankers and blights have gained attention in temperate woodlands and crops, the scope for fungal pathogens of animals and their potential threat has received far less attention. With a shifting climate, the threat from fungal pathogens is predicted to increase in the future, thus understanding the spread of fungi over landscapes as well as taxa that may be at risk is of particular importance. Cave ecosystems provide potential refugia for various fungi, and roosts for bats. With their well vascularized wings and wide-ranging distributions, bats present potential fungal vectors. Furthermore, whilst bat immune systems are generally robust to bacterial and viral pathogens, they can be susceptible to fungal pathogens, particularly during periods of stress such as hibernation. Here we explore why bats are important and interesting vectors for fungi across landscapes and discuss knowledge gaps that require further research.

Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats

The advent of next generation sequencing technologies (NGS) has greatly accelerated our understanding of critical aspects of organismal biology from non-model organisms. Bats form a particularly interesting group in this regard, as genomic data have helped unearth a vast spectrum of idiosyncrasies in bat genomes associated with bat biology, physiology, and evolution. Bats are important bioindicators and are keystone species to many eco-systems. They often live in proximity to humans and are frequently associated with emerging infectious diseases, including the COVID-19 pandemic. Nearly four dozen bat genomes have been published to date, ranging from drafts to chromosomal level assemblies. Genomic investigations in bats have also become critical towards our understanding of disease biology and host-pathogen coevolution. In addition to whole genome sequencing, low coverage genomic data like reduced representation libraries, resequencing data, etc. have contributed significantly towards our understanding of the evolution of natural populations, and their responses to climatic and anthropogenic perturbations. In this review, we discuss how genomic data have enhanced our understanding of physiological adaptations in bats (particularly related to ageing, immunity, diet, etc.), pathogen discovery, and host pathogen co-evolution. In comparison, the application of NGS towards population genomics, conservation, biodiversity assessment, and functional genomics has been appreciably slower. We reviewed the current areas of focus, identifying emerging topical research directions and providing a roadmap for future genomic studies in bats.

Role of Brazilian bats in the epidemiological cycle of potentially zoonotic pathogens

Bats (Chiroptera) are flying mammals of great biodiversity and habits. These characteristics contribute for them being natural reservoirs and part of the epidemiological cycle of several potentially zoonotic pathogens, such as viruses, protozoa, fungi and bacteria. Brazil hosts approximately 15% of the world's bat diversity, with 181 distinct species, 68 genera and 9 families. About 60% of infectious diseases in humans are of zoonotic origin and, in the last decades, the detection of zoonotic pathogens in bats and their environment has been reported, such as Rabies virus (RABV) and Histoplasma capsulatum. Thus, the aim of this work was to review the reports of zoonotic pathogens associated with bats in Brazil in the past ten years. We reviewed the main pathogenic microorganisms described and the species of bats most frequently involved in the epidemiological cycles of these zoonotic agents. The obtained data show an upward trend in the detection of zoonotic pathogens in Brazilian bats, such as RABV, Bartonella sp., Histoplasma capsulatum and Leishmania spp., with emphasis on the bat species Artibeus lituratus, Carollia perspicillata, Desmodus rotundus and Molossus molossus. These findings highlight the importance of monitoring bat-associated microrganisms to early identify pathogens that may threaten bat populations, including potentially zoonotic microrganisms, emphasizing the importance of the One Health approach to prevent and mitigate the risks of the emergence of zoonotic diseases.

In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response

Introduction

Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown.

Methods

Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge.

Results

We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities.

Conclusion

Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.

An Overview of Anthropogenic Actions as Drivers for Emerging and Re-Emerging Zoonotic Diseases

Population growth and industrialization have led to a race for greater food and supply productivity. As a result, the occupation and population of forest areas, contact with wildlife and their respective parasites and vectors, the trafficking and consumption of wildlife, the pollution of water sources, and the accumulation of waste occur more frequently. Concurrently, the agricultural and livestock production for human consumption has accelerated, often in a disorderly way, leading to the deforestation of areas that are essential for the planet's climatic and ecological balance. The effects of human actions on other ecosystems such as the marine ecosystem cause equally serious damage, such as the pollution of this habitat, and the reduction of the supply of fish and other animals, causing the coastal population to move to the continent. The sum of these factors leads to an increase in the demands such as housing, basic sanitation, and medical assistance, making these populations underserved and vulnerable to the effects of global warming and to the emergence of emerging and re-emerging diseases. In this article, we discuss the anthropic actions such as climate changes, urbanization, deforestation, the trafficking and eating of wild animals, as well as unsustainable agricultural intensification which are drivers for emerging and re-emerging of zoonotic pathogens such as viral (Ebola virus, hantaviruses, Hendravirus, Nipah virus, rabies, and severe acute respiratory syndrome coronavirus disease-2), bacterial (leptospirosis, Lyme borreliosis, and tuberculosis), parasitic (leishmaniasis) and fungal pathogens, which pose a substantial threat to the global community. Finally, we shed light on the urgent demand for the implementation of the One Health concept as a collaborative global approach to raise awareness and educate people about the science behind and the battle against zoonotic pathogens to mitigate the threat for both humans and animals.

Henipavirus Immune Evasion and Pathogenesis Mechanisms: Lessons Learnt from Natural Infection and Animal Models

Nipah henipavirus (NiV) and Hendra henipavirus (HeV) are zoonotic emerging paramyxoviruses causing severe disease outbreaks in humans and livestock, mostly in Australia, India, Malaysia, Singapore and Bangladesh. Both are bat-borne viruses and in humans, their mortality rates can reach 60% in the case of HeV and 92% for NiV, thus being two of the deadliest viruses known for humans. Several factors, including a large cellular tropism and a wide zoonotic potential, con-tribute to their high pathogenicity. This review provides an overview of HeV and NiV pathogenicity mechanisms and provides a summary of their interactions with the immune systems of their different host species, including their natural hosts bats, spillover-hosts pigs, horses, and humans, as well as in experimental animal models. A better understanding of the interactions between henipaviruses and their hosts could facilitate the development of new therapeutic strategies and vaccine measures against these re-emerging viruses.

The Role of Micronutrients and Toxic Metals in the Management of Epidemics in Cambodia

The illegal trade of wildlife in SE Asia has been identified as the likely cause of the COVID-19 pandemic. We reviewed 198 papers on the current COVID pandemic in Cambodia, diseases such as avian influenza and Nipah virus, most likely to develop into a new pandemic in Cambodia, and common features of disease that require mitigation. Artisanal goldmining uses pure mercury in the areas where wildlife is smuggled to China. Moreover, 30-40% of Cambodians are zinc deficient. High levels of arsenic in irrigation water (>1000 µg/L) are associated with very low levels of zinc in rice (5 µg/g) and rice is the primary staple food for the region. Brown rice from nine of 15 paddy fields in the arsenic zone of Cambodia had double the new guidelines of 100 µg/kg inorganic arsenic for children's food in the EU and USA. The combination of deficiencies of essential micronutrients like zinc and pervasive presence of arsenic and mercury has the potential to compromise the immunity of many Cambodians. Innovative solutions are suggested to improve micronutrient nutrition. Toxins that suppress the immune system must be better managed to reduce the virulence of pathogens. Cambodia was not likely the source of the COVID-19 but does have problems that could result in a new pandemic.

Common Themes in Zoonotic Spillover and Disease Emergence: Lessons Learned from Bat- and Rodent-Borne RNA Viruses

Rodents (order Rodentia), followed by bats (order Chiroptera), comprise the largest percentage of living mammals on earth. Thus, it is not surprising that these two orders account for many of the reservoirs of the zoonotic RNA viruses discovered to date. The spillover of these viruses from wildlife to human do not typically result in pandemics but rather geographically confined outbreaks of human infection and disease. While limited geographically, these viruses cause thousands of cases of human disease each year. In this review, we focus on three questions regarding zoonotic viruses that originate in bats and rodents. First, what biological strategies have evolved that allow RNA viruses to reside in bats and rodents? Second, what are the environmental and ecological causes that drive viral spillover? Third, how does virus spillover occur from bats and rodents to humans?