The cave microbiome as a source for drug discovery: Reality or pipe dream?

Subterranean marvels: microbial communities in caves and underground mines and their promise for natural product discovery

Covering: 2014 to 2024Since the dawn of human history, caves have played an intimate role in our existence. From our earliest ancestors seeking shelter from the elements to more recent generations harnessing cave substances for medicinal purposes, caves have served as essential resources and havens. The last 40 years of geomicrobiology research has replaced the outdated perception of subterranean environments as lifeless and unchanging with the realization that vibrant microbial communities have adapted to thrive in extreme conditions over millions of years. The ability of subterranean microbial communities to withstand nutrient deprivation and darkness creates a unique reservoir of untapped biosynthetic potential. These communities offer exciting prospects for medicine (e.g., antimicrobial and antitumor therapies) and biotechnology (e.g., redox chemical properties and biomineralization). This article highlights the significance of caves and mines as reservoirs of microbial diversity, the potential impact of their bioactive compounds on the fields of healthcare and biotechnology, and the significant challenges that must be overcome to access and harness the biotechnological potential of subterranean microbial communities. Additionally, it emphasizes the conservation efforts needed to protect these delicate ecosystems, ensuring the preservation of both ancient traditions and tomorrow's medicines.

Cis-3-Indoleacrylic Acid: A Nematicidal Compound from Streptomyces youssoufiensis YMF3.862 as V-ATPase Inhibitor on Meloidogyne incognita

The application of the bionematicides derived from microorganisms and their secondary metabolites represents a promising strategy for managing root-knot nematodes. In this study, a nematicidal compound, cis-3-indoleacrylic acid, was isolated from Streptomyces youssoufiensis YMF3.862. This compound caused Meloidogyne incognita juveniles to have swollen bodies with apparent cracks on the cuticle surface. The LC50 value of cis-3-indoleacrylic acid against juveniles was 16.31 μg/mL 24 h of post-treatment. Cis-3-indoleacrylic acid at 20 μg/mL significantly inhibited V-ATPase expression and remarkably decreased enzyme activity by 84.41%. As an inhibitor of V-ATPase, cis-3-indoleacrylic acid caused significant H+ accumulation in nematode bodies, resulting in lower intracellular pH values and higher extracellular pH values of M. incognita. Application of 50 μg/mL cis-3-indoleacrylic acid generated a 71.06% control efficiency against M. incognita on tomatoes. The combination results of this study indicated that cis-3-indoleacrylic acid can be developed as a natural nematicide for controlling M. incognita.

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.

Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave

BACKGROUND

Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.

RESULTS

We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.

CONCLUSIONS

These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.

Cryosphere: a frozen home of microbes and a potential source for drug discovery

The world is concerned about the emergence of pathogens and the occurrence and spread of antibiotic resistance among pathogens. Drug development requires time to combat these issues. Consequently, drug development from natural sources is unavoidable. Cryosphere represents a gigantic source of microbes that could be the bioprospecting source of natural products with unique scaffolds as molecules or drug templates. This review focuses on the novel source of drug discovery and cryospheric environments as a potential source for microbial metabolites having potential medicinal applications. Furthermore, the problems encountered in discovering metabolites from cold-adapted microbes and their resolutions are discussed. By adopting modern practical approaches, the discovery of bioactive compounds might fulfill the demand for new drug development.

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.

Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves

Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.

Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity

The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.

Stalactites Core Prospect as Environmental "Microbial Ark": The Actinomycetota Diversity Paradigm, First Reported from a Greek Cave

Speleothems found in caves worldwide are considered the natural libraries of paleontology. Bacteria found in these ecosystems are generally limited to Proteobacteria and Actinomycetota, but rare microbiome and "Dark Matter" is generally under-investigated and often neglected. This research article discusses, for the first time to our knowledge, the diachronic diversity of Actinomycetota entrapped inside a cave stalactite. The planet's environmental microbial community profile of different eras can be stored in these refugia (speleothems). These speleothems could be an environmental "Microbial Ark" storing rare microbiome and "Dark Matter" bacterial communities evermore.

Isolation, antibacterial screening, and identification of bioactive cave dwelling bacteria in Fiji

Bacteria are well known producers of bioactive secondary metabolites, including some of the most effective antibiotics in use today. While the caves of Oceania are still largely under-explored, they form oligotrophic and extreme environments that are a promising source for identifying novel species of bacteria with biologically active compounds. By using selective media that mimicked a cave environment, and pretreatments that suppressed the growth of fast-growing bacteria, we have cultured genetically diverse bacteria from a limestone cave in Fiji. Partial 16S rRNA gene sequences from isolates were determined and compared with 16S rRNA gene sequences in EzBioCloud and SILVA data bases. Fifty-five isolates purified from culture had Actinomycete-like morphologies and these were investigated for antibacterial activity. Initial screening using a cross streak test with pathogenic bacteria indicated that 34 of the isolates had antibacterial properties. The best matches for the isolates are bacteria with potential uses in the manufacture of antibiotics and pesticides, in bioremediation of toxic waste, in biomining, in producing bioplastics, and in plant growth promotion. Nineteen bacteria were confirmed as Actinomycetes. Thirteen were from the genus Streptomyces and six from genera considered to be rare Actinomycetes from Pseudonocardia, Kocuria, Micromonospora, Nonomuraea. Ten isolates were Firmicutes from the genera Bacillus, Lysinbacillus, Psychrobacillus and Fontibacillus. Two were Proteobacteria from the genera Mesorhizobium and Cupriavidus. Our findings identify a potentially rich source of microbes for applications in biotechnologies.

Antifungal metabolites, their novel sources, and targets to combat drug resistance

Excessive antibiotic prescriptions as well as their misuse in agriculture are the main causes of antimicrobial resistance which poses a growing threat to public health. It necessitates the search for novel chemicals to combat drug resistance. Since ancient times, naturally occurring medicines have been employed and the enormous variety of bioactive chemicals found in nature has long served as an inspiration for researchers looking for possible therapeutics. Secondary metabolites from microorganisms, particularly those from actinomycetes, have made it incredibly easy to find new molecules. Different actinomycetes species account for more than 70% of naturally generated antibiotics currently used in medicine, and they also produce a variety of secondary metabolites, including pigments, enzymes, and anti-inflammatory compounds. They continue to be a crucial source of fresh chemical diversity and a crucial component of drug discovery. This review summarizes some uncommon sources of antifungal metabolites and highlights the importance of further research on these unusual habitats as a source of novel antimicrobial molecules.

Major impacts of caving activities on cave microbial diversity: case study of Morca Cave, Turkey

Some of microorganisms identified in cave ecosystems have been reported to play a permanent and strategic role for maintaining life of these environments. Human entrance into caves can induce some changes of cave physicochemical parameters which ultimately impacts the living organisms. In these facts, for the first time, Morca Cave was explored in a purpose to evaluate the impacts that can be caused by the human activities on microbial diversity in a limited period of time. Morca is a karts cave located in the Taşeli Plateau in the Middle Taurus mountains in Turkey. The first entrance into this cave was in 2018, and expeditors reached to - 500 m. During the second expedition in 2019, a camp was established at the - 1040-m depth during 4 days. In order to evaluate the human impacts in a new explored cave, this camping depth is chosen to be our studied area because it was its first entrance. Before the installation and at the end of the camp, sediments and surface samples were taken from different points of the camp area and around. Sequencing of 16 s rRNA of each sample to isolate DNA by using the next-generation sequencing (NGS) method was performed. The profile of the microbial diversity before the camping revealed that the class Thermoplasmata was dominated the archaea group and Gammaproteobacteria and Alphaproteobacteria were the most dominant bacterial classes. After the camp, most studied sites were noted with a decrease of microbial diversity especially the previous cited classes strains. Bacteria belonging to Bacilli class have increased after the camp. Increase of bacteria that are belonging to Bacteroidia has also observed in the most active areas. This present study highlight how cave microbial diversity can respond to the human activities within a short period inside a closed cave. Furthermore, it may constitute a solid basis and support on the improvement of techniques for cave management and expedition planning for the conservation of cave nature.

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.

Cultivable microbial diversity in speleothems using MALDI-TOF spectrometry and DNA sequencing from Krem Soitan, Krem Lawbah, Krem Mawpun, Khasi Hills, Meghalaya, India

The microbial diversity in the Indian caves is inadequately characterized. This study reports on the culturable microbial communities in caves from the Indian sub-continent. This study aims to expand the current understanding of bacterial diversity in the speleothems and wall deposits from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. A culture-dependent approach was employed for elucidating the community structure in the caves using MALDI-TOF spectrometry and 16S rRNA gene sequencing. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. A total 91% of the bacterial diversity was dominated by Proteobacteria (61%) and Actinobacteria (30%). In addition, bacterial phyla include Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%) were found in the samples. At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.

Microbial ecology of tourist Paleolithic caves

Microorganisms colonize caves extensively, and in caves open for tourism they may cause alterations on wall surfaces. This is a major concern in caves displaying Paleolithic art, which is usually fragile and may be irremediably damaged by microbial alterations. Therefore, many caves were closed for preservation purposes, e.g. Lascaux (France), Altamira (Spain), while others were never opened to the public to avoid microbial contamination, e.g. Chauvet Cave (France), etc. The recent development of high-throughput sequencing technologies allowed several descriptions of cave microbial diversity and prompted the writing of this review, which focuses on the cave microbiome for the three domains of life (Bacteria, Archaea, microeukaryotes), the impact of tourism-related anthropization on microorganisms in Paleolithic caves, and the development of microbial alterations on the walls of these caves. This review shows that the microbial phyla prevalent in pristine caves are similar to those evidenced in water, soil, plant and metazoan microbiomes, but specificities at lower taxonomic levels remain to be clarified. Most of the data relates to Bacteria and Fungi, while other microeukaryotes and Archaea are poorly documented. Tourism may cause shifts in the microbiota of Paleolithic caves, but larger-scale investigation are required as these shifts may differ from one cave to the next. Finally, different types of alterations can occur in caves, especially in Paleolithic caves. Many microorganisms potentially involved have been identified, but diversity analyses of these alterations have not always included a comparison with neighboring unaltered zones as controls, making such associations uncertain. It is expected that omics technologies will also allow a better understanding of the functional diversities of the cave microbiome. This will be needed to decipher microbiome dynamics in response to touristic frequentation, to guide cave management, and to identify the most appropriate reclamation approaches to mitigate microbial alterations in tourist Paleolithic caves.

The diversity of microbes and prediction of their functions in karst caves under the influence of human tourism activities-a case study of Zhijin Cave in Southwest China

Microorganisms, sensitive to the surrounding environment changes, show how the cave environment can be impacted by human activities. Zhijin Cave, featured with the most well-developed karst landform in China, has been open to tourists for more than 30 years. This study explored the microbial diversity in a karst cave and the impacts of tourism activities on the microbial communities and the community structures of bacteria and archaea in three niches in Zhijin Cave, including the mixture of bacteria and cyanobacteria on the rock wall, the aquatic sediments, and the surface sediments, using 16S rRNA high-throughput sequencing technology. It was found that Actinobacteriota and Proteobacteria were the dominant bacteria in the cave and Crenarchaeota and Thermoplasmatota were the dominant archaea. The correlation between microorganisms and environmental variables in the cave showed that archaea were more affected by pH and ORP than bacteria and F^-, Cl^-, NO₃^-, and SO₄^2- were all positively relevant to the distribution of most bacteria and archaea in the cave. PICRUSt's prediction of microbial functions also indicated that abundance of the bacteria's functions was higher than that of the archaea. The intention of this study was to improve the understanding, development, and protection of microbial resources in caves.

Sulfur-Containing Phenolic Compounds from the Cave Soil-Derived Aspergillus fumigatus GZWMJZ-152

Six new sulfur-containing phenolic compounds (1-6) and their putative metabolic precursors (7-9) were isolated from the cave soil-derived fungus Aspergillus fumigatus GZWMJZ-152. Compound 1 represents an unusual benzophenone-diketopiperazine hybrid via a thioether linker, while compound 2 contains a naturally rare sulfoxide group. Both compounds 2 and 3 were initially isolated as racemic mixtures and then purified as the enantiomerically pure (+)-2, (-)-2, (+)-3, and (-)-3, respectively. Their structures, including absolute configurations, were elucidated by spectroscopic analysis, X-ray diffraction, and the calculations of electronic circular dichroism. The antioxidant activity of compounds 1-9 was evaluated based on oxygen radical absorbance capacity, 2,2-diphenyl-1-picrylhydrazyl radical scavenging, and the protective effect on the PC12 cell line against H₂O₂-induced damage. Compounds 5-7 and 9 showed radical-scavenging activity against 2,2-diphenyl-1-picrylhydrazyl free radicals with the IC₅₀ values of 3.45 ± 0.02, 23.73 ± 0.08, 18.90 ± 0.16, and 17.27 ± 0.15 μM, respectively. Compounds (±)-2, 4, 7, and 8 exhibited potent antioxidant capacity with oxygen radical absorbance capacity values of 1.73 ± 0.13, 1.65 ± 0.03, 6.14 ± 0.35, and 1.55 ± 0.04 μmol TE/μmol, respectively. Compounds (±)-2 and (±)-3 also exhibited protective effects on oxidative injury of PC12 cells induced by H₂O₂.

Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments

The environmental conditions of caves shape microbiota. Within caves' microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves' actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves' actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes' outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens.

Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use

Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source of interest for various research groups including geologists, chemists, ecologists, or microbiologists. The adaptations of cave-dwelling organisms applied to their survival are complex and some of their properties show potential to be used in various areas of human life. Secondary metabolites produced by cave’s bacteria show strong antimicrobial, anti-inflammatory, or anticancer properties. Furthermore, bacteria that can induce mineral precipitation could be used in the construction industry and for neutralization of radioisotopes. In this review we focus on bacteria and algae present in cave ecosystems, their role in shaping such specific environment, and their biotechnological and medical potential.

Microbial Interactions Drive Distinct Taxonomic and Potential Metabolic Responses to Habitats in Karst Cave Ecosystem

The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave.

IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.

Isolation and characterization of novel Streptomyces strain from Algeria and its in-vitro antimicrobial properties against microbial pathogens

BACKGROUND

The constant development of microbial resistance to the traditional antimicrobial agents and the emergence of new infectious diseases justify the urgent need for new effective antimicrobial molecules. However, the irrational use of antibiotics increases microbial resistance dramatically and along with that the frequency of mortality associated with infections is higher. Therefore, to combat the antimicrobial resistance, the screening of compounds with novel chemical structures is essential. This study intended to determine the antimicrobial potential of Streptomyces GLD22 strain isolated from Algeria.

METHODS

The characterization of Streptomyces strain GLD22 was performed by physiological, biochemical and molecular tests. The antimicrobial activity was tested by the well diffusion method and the minimum inhibitory concentration value calculation were performed using broth micro dilution technique. The extracellular metabolites profiling was done using GC-MS.

RESULTS

Physiological, biochemical and phylogenetic analysis confirmed that the strain GLD22 showed maximum identity towards Streptomyces species. The extra cellular metabolites revealed their antimicrobial activity at 1 mg/ml for Klebsiella pneumoniae, Pseudomonas aeruginosa and Escherichia coli, whereas Staphylococcus aureus, Bacillus cereus and Bacillus subtilis documented 0.5, 1 and 1 mg/ml respectively. GC-MS analysis confirmed that 2-tert-butyl-4,6-bis(3,5-di-tert-butyl-4-hydroxybenzyl) phenol, Dibutyl phthalate and Cyclo(leucyloprolyl) were the major drug molecules present in the extract.

CONCLUSION

The novel Streptomyces strain GLD22 recovered from the Gueldaman cave of Algeria showed better antimicrobial activity towards both Gram positive and Gram negative pathogens. Interestingly, the MIC values were comparable with the standard drug molecules. In addition, the identification of active metabolites present in the crude extracts was an advantage.

Characterisation of Environmental Biofilms Colonising Wall Paintings of the Fornelle Cave in the Archaeological Site of Cales

Caves present unique habitats for the development of microbial communities due to their peculiar environmental conditions. In caves decorated with frescoes, the characterization of microbial biofilm is important to better preserve and safeguard such artworks. This study aims to investigate the microbial communities present in the Fornelle Cave (Calvi Risorta, Caserta, Italy) and their correlation with environmental parameters. The cave walls and the wall paintings have been altered by environmental conditions and microbial activity. We first used light microscopy and scanning electron microscopy (SEM) and X-ray diffraction to characterise the biofilm structure and the mineral composition of substrata, respectively. Then, using both culture-dependent (Sanger sequencing) and culture-independent (automated ribosomal intergenic spacer analysis, ARISA) molecular methods, we demonstrated that the taxonomic composition of biofilms was different across the three substrata analysed and, in some cases, positively correlated with some environmental parameters. We identified 47 taxa in the biofilm samples, specifically 8 bacterial, 18 cyanobacterial, 14 algal and 7 fungal taxa. Fungi showed the highest number of ARISA types on the tuff rock, while autotrophic organisms (cyanobacteria and algae) on the frescoes exposed to light. This study confirms that caves constitute a biodiversity-rich environment for microbial taxa and that, in the presence of wall paintings, taxonomic characterization is particularly important for conservation and restoration purposes.

First Speleomycological Study on the Occurrence of Psychrophilic and Psychrotolerant Aeromycota in the Brestovská Cave (Western Tatras Mts., Slovakia) and First Reports for Some Species at Underground Sites

Most underground ecosystems are heterotrophic, fungi in these objects are dispersed in the air in the form of spores, and they may be potentially hazardous to mammals. Research in underground sites has focused on mesophilic airborne fungi and only a few concerned cold-adapted species. Therefore, the goal of our research was the first report of psychrophilic and psychrotolerant aeromycota in the Brestovská Cave using culture-based techniques with genetic and phenotypic identification. Plates with PDA medium containing sampled biological material were incubated at 8 ± 0.5 °C. The density of mycobiota inside the cave ranged from 37.4 to 71 CFU 1 m-3 of air and 63.3 CFU 1 m-3 of air outside the cave. Thus, the level of fungal spores did not exceed the standards for the mycological quality of the air. A total of 18 species were isolated during the study, and some species may be potentially dangerous to people with weakened immune system. All fungal species were present inside the cave and only seven of them were outside. Cladosporium cladosporioides dominated in the external air samples and Mortierella parvispora was cultured most frequently from internal air samples. To our knowledge, this is the first discovery of the fungal species such as Coniothyrium pyrinum, Cystobasidium laryngis, Filobasidium wieringae, Leucosporidium drummii, M. parvispora, Mrakia blollopis, Nakazawaea holstii, and Vishniacozyma victoriae in the air inside the underground sites. Moreover, C. pyrinum, C. laryngis, L. drummii, M. blollopis, and N. holstii have never been detected in any component of the underground ecosystems. There are possible reasons explaining the detection of those species, but global warming is the most likely.

Genome Mining and Characterization of Biosynthetic Gene Clusters in Two Cave Strains of Paenibacillus sp

The genome sequencing and mining of microorganisms from unexplored and extreme environments has become important in the process of identifying novel biosynthetic pathways. In the present study, the biosynthetic potential of Paenibacillus sp. strains 23TSA30-6 and 28ISP30-2 was investigated. Both strains were isolated from the deep oligotrophic Krubera-Voronja Cave and were found to be highly active against both Gram-positive and Gram-negative bacteria. Genome mining revealed a high number of biosynthetic gene clusters in the cave strains: 21 for strain 23TSA30-6 and 19 for strain 28ISP30-2. Single clusters encoding the biosynthesis of phosphonate, terpene, and siderophore, as well as a single trans-AT polyketide synthase/non-ribosomal peptide synthetase, were identified in both genomes. The most numerous clusters were assigned to the biosynthetic pathways of non-ribosomal peptides and ribosomally synthesized and post-translationally modified peptides. Although four non-ribosomal peptide synthetase gene clusters were predicted to be involved in the biosynthesis of known compounds (fusaricidin, polymyxin B, colistin A, and tridecaptin) of the genus Paenibacillus, discrepancies in the structural organization of the clusters, as well as in the substrate specificity of some adenylation domains, were detected between the reference pathways and the clusters in our study. Among the clusters involved in the biosynthesis of ribosomally synthesized peptides, only one was predicted to be involved in the biosynthesis of a known compound: paenicidin B. Most biosynthetic gene clusters in the genomes of the cave strains showed a low similarity with the reference pathways and were predicted to represent novel biosynthetic pathways. In addition, the cave strains differed in their potential to encode the biosynthesis of a few unique, previously unknown compounds (class II lanthipeptides and three non-ribosomal peptides). The phenotypic characterization of proteinaceous and volatile compounds produced by strains 23TSA30-6 and 28ISP30-2 was also performed, and the results were compared with those of genome mining.

Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave

Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.

Let research on subterranean habitats resonate!

Whereas scientists interested in subterranean life typically insist that their research is exciting, adventurous, and important to answer general questions, this enthusiasm and potential often fade when the results are translated into scientific publications. This is because cave research is often written by cave scientists for cave scientists; thus, it rarely “leaves the cave”. However, the status quo is changing rapidly. We analysed 21,486 articles focused on subterranean ecosystems published over the last three decades and observed a recent, near-exponential increase in their annual citations and impact factor. Cave research is now more often published in non-specialized journals, thanks to a number of authors who are exploiting subterranean habitats as model systems for addressing important scientific questions. Encouraged by this positive trend, we here propose a few personal ideas for improving the generality of subterranean literature, including tips for framing broadly scoped research and making it accessible to a general audience, even when published in cave-specialized journals. Hopefully, this small contribution will succeed in condensing and broadcasting even further the collective effort taken by the subterranean biology community to bring their research “outside the cave”.

The cutaneous microbiota of bats has in vitro antifungal activity against the white nose pathogen

Since its introduction into the USA, Pseudogymnoascus destructans (Pd), the fungal pathogen of white-nose syndrome, has killed millions of bats. Recently, bacteria capable of inhibiting the growth of Pd have been identified within bat microbial assemblages, leading to increased interest in elucidating bacterial assemblage-pathogen interactions. Our objectives were to determine if bat cutaneous bacteria have antifungal activity against Pd, and correlate differences in the bat cutaneous microbiota with the presence/absence of Pd. We hypothesized that the cutaneous microbiota of bats is enriched with antifungal bacteria, and that the skin assemblage will correlate with Pd status. To test this, we sampled bat microbiota, adjacent roost surfaces and soil from Pd positive caves to infer possible overlap of antifungal taxa, we tested these bacteria for bioactivity in vitro, and lastly compared bacterial assemblages using both amplicon and shotgun high-throughput DNA sequencing. Results suggest that the presence of Pd has an inconsistent influence on the bat cutaneous microbial assemblage across sites. Operational taxonomic units (OTUs) that corresponded with cultured antifungal bacteria were present within all sample types but were significantly more abundant on bat skin relative to the environment. Additionally, the microbial assemblage of Pd negative bats was found to have more OTUs that corresponded to antifungal taxa than positive bats, suggesting an interaction between the fungal pathogen and cutaneous microbial assemblage.

Diversity, Ecology, and Prevalence of Antimicrobials in Nature

Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.

Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches

Karst caves, considering to be the "arks" of biodiversity, often contain high levels of endemism. In the present study, the actinobacterial community in Shuanghe Cave, the longest cave in Asia, was analyzed for the first-time using culture-dependent and -independent (16S rRNA amplicon sequencing) approaches. The amplicon sequencing analysis revealed a broad taxonomic diversity in Shuanghe Cave, including 19 phyla (predominantly Actinobacteria) and 264 different genera. While the culture-dependent method got the unrepresentative but supplemental result, a total of 239 actinomycetes were isolated and were identified to seven genera based on culture features and 16S rRNA tests. Among the three habitats (soil, rock soil, and bat guano), the dominant phyla did not differ significantly, while the dominant genus community varied among different habitats, and the richness in soil and rock soil samples was higher than that in bat guano. Furthermore, 16 isolate strains showed antimicrobial activity, especially, the strain S142 (Streptomyces badius) and S761 (Actinoplanes friuliensis) exhibited the most promising activity against various pathogens. Overall, this work showed the abundant bacterial diversity and the antimicrobial potential of the isolates from the Shuanghe Cave.

Screening and Transcriptional Analysis of Polyketide Synthases and Non-ribosomal Peptide Synthetases in Bacterial Strains From Krubera-Voronja Cave

Identification of novel bioactive compounds represents an important field in modern biomedical research. Microorganisms of the underexplored environments, such as deserts, hot springs, oceans, and caves are highly promising candidates for screening such metabolites. Screening for biosynthetic genes is the most effective strategy to characterize bioactivity in a certain environment. However, knowledge is either scant or non-existent about the expression of the biosynthetic genes encoding for various bioactive compounds in the microorganisms from the caves. The aim of the current study was to screen for the genes of polyketide synthases and non-ribosomal peptide synthetases in Krubera–Voronja Cave (43.4184 N 40.3083 E, Western Caucasus) bacterial isolates as well as to evaluate the expression of these genes under laboratory conditions. In total, 91 bacterial strains isolated from the cave were screened for the presence of polyketide synthase and non-ribosomal peptide synthetase genes. Phenotypically inactive strains were the main focus (the test group) of our study, while the strains with the identified antibacterial activity served as the control group. Our PCR-based screening clearly showed that the majority of the strains harbored at least one biosynthetic gene. Prediction of the putative products allowed us to identify bioactive compounds with antibacterial, anticancer, antifungal, anti-inflammatory, antimycoplasmic, antiviral, insecticidal, and thrombolytic activity. For most polyketide synthases and non-ribosomal peptide synthetases, putative products could not be predicted; they are unknown. Qualitative transcriptional analysis did not show substantial differences between the test group and the control group of the strains. One to four biosynthetic genes were constitutively expressed in all the tested strains, irrespective of the group. Quantitative transcriptional analysis of the constitutively expressed biosynthetic genes demonstrated that the expression of a particular gene could be affected by both the amount of the nutrients in the culture medium and the growth phase.

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

Caves are typified by their permanent darkness and a shortage of nutrients. Consequently, bacteria play an important role in sustaining such subsurface ecosystems by dominating primary production and fueling biogeochemical cycles. China has one of the world’s largest areas of karst topography in the Yunnan-Guizhou Plateau, yet the bacteriomes in these karst caves remain unexplored. In this study, bacteriomes of eight karst caves in southwest China were examined, and co-occurrence networks of cave bacterial communities were constructed. Results revealed abundant and diversified bacterial communities in karst caves, with Proteobacteria, Actinobacteria, and Firmicutes being the most abundant phyla. Statistical analysis revealed no significant difference in bacteriomes among the eight caves. However, a PCoA plot did show that the bacterial communities of 128 cave samples clustered into groups corresponding to sampling types (air, water, rock, and sediment). These results suggest that the distribution of bacterial communities is driven more by sample types than the separate caves from which samples were collected. Further community-level composition analysis indicated that Proteobacteria were most dominant in water and air samples, while Actinobacteria dominated the sediment and rock samples. Co-occurrence analysis revealed highly modularized assembly patterns of the cave bacterial community, with Nitrosococcaceae wb1-P19, an uncultured group in Rokubacteriales, and an uncultured group in Gaiellales, being the top-three keystone members. These results not only expand our understanding of cave bacteriomes but also inspires functional exploration of bacterial strains in karst caves.

Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

Background

Due to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive. However, it has been well documented that microorganisms play important roles in cave development. Survival of microbes in this unique habitat likely involves a broad range of adaptive capabilities. Recently, cave microbiomes all over the world are of great scientific interest. However, the majority of investigations focused mostly on small subunit ribosomal RNA (16S rRNA) gene, leaving the ecological role of the microbial community largely unknown. Here, we are particularly interested in exploring the taxonomic composition and metabolic potential of microorganisms in soil from Manao-Pee cave, a subterranean limestone cave in the western part of Thailand, by using high-throughput shotgun metagenomic sequencing.

Results

From taxonomic composition analysis using ribosomal RNA genes (rRNA), the results confirmed that Actinobacteria (51.2%) and Gammaproteobacteria (24.4%) were the dominant bacterial groups in the cave soil community. Metabolic potential analysis, based on six functional modules of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, revealed that functional genes involved in microbial metabolisms are highly represented in this community (40.6%). To better understand how microbes thrive under unfavorable cave condition, we focused on microbial energy metabolism. The results showed that microbial genes involved in oxidative phosphorylation were the most dominant (28.8%) in Manao-Pee cave, and were followed by methane metabolism (20.5%), carbon fixation (16.0%), nitrogen metabolism (14.7%), and sulfur metabolism (6.3%). In addition, microbial genes involved in xenobiotic biodegradation (26 pathways) and in production of secondary metabolites (27 pathways) were also identified.

Conclusion

In addition to providing information on microbial diversity, we also gained insights into microbial adaptations and survival strategies under cave conditions. Based on rRNA genes, the results revealed that bacteria belonging to the Actinobacteria and Gammaproteobacteria were the most abundant in this community. From metabolic potential analysis, energy and nutrient sources that sustain diverse microbial population in this community might be atmospheric gases (methane, carbon dioxide, nitrogen), inorganic sulfur, and xenobiotic compounds. In addition, the presence of biosynthetic pathways of secondary metabolites suggested that they might play important ecological roles in the cave microbiome.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1521-8) contains supplementary material, which is available to authorized users.

Syn-2, 3-diols and anti-inflammatory indole derivatives from Streptomyces sp. CB09001

Two new natural diols, (2S, 3S, 4S)-4-methyl-1-phenylhexane-2,3-diol (1) and (2S, 3S)-4-methyl-1-phenylpentane-2,3-diol (2), together with five known compounds, xenocyloins B-D (3-5), lumichrome (6) and thymidine (7) were isolated from Streptomyces sp. CB09001. The absolute configurations of 1 and 2 were established by crystallographic structure analysis. The anti-inflammatory effects of 1-7 were also investigated in RAW246.7 murine macrophage cells stimulated by lipopolysaccharide. The indole derivative xenocyloin B (3) significantly inhibited inducible nitric oxide synthase expression in RAW264.7 cells and could be a potential anti-inflammatory drug lead.

Profiling the Bacterial Diversity in a Typical Karst Tiankeng of China

While karst tiankengs have a higher capacity to act as safe havens for biodiversity in changing climates, little is known about their soil microorganisms. To fill this gap, we investigate the distribution and driving factors of the bacterial community in karst tiankeng systems. There is a significant difference in the soil characteristics between the inside and the outside of a karst tiankeng. At the karst tiankeng considered in this study, the bacterial composition, in terms of the operational taxonomic unit (OTU), was found to be significantly different in different soil samples, taken from diverse sampling sites within the collapsed doline or the external area, and showed a high habitat heterogeneity. The dominant phylum abundances vary with the sampling sites and have their own indicator taxa from phylum to genus. Unlike the primary controlling factors of plant diversity, the microclimate (soil moisture and temperature), soil pH, and slope dominated the distribution of the bacterial community in karst tiankeng systems. Our results firstly showed the distribution characteristics of bacterial communities and then revealed the importance of microhabitats in predicting the microbial distribution in karst tiankeng systems.

Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4

The terrestrial subsurface microbiome has gained considerable amount of interests in the recent years because of its rich potential resource for biomining novel genes coding for metabolites possessing antimicrobial activities. In our previous study, we identified two Streptomyces isolates, designated as ICC1 and ICC4, from the Iron Curtain Cave, Chilliwack, Canada that exhibited antagonistic activities against the multidrug resistant strains of Escherichia coli. In this study, the genomes of these two isolates were sequenced by Illumina MiSeq, assembled and annotated. The genes associated with secondary metabolite production were identified and annotated using the bioinformatics platforms antiSMASH and BAGEL. ICC1 and ICC4 were then cultivated and ICC1 metabolome characterized by UHPLC-ESI-HRMS. The Global Natural Products Social Molecular Networking was used to identify metabolites based on the MS/MS spectral data. ICC1 and ICC4 showed a high level of sequence identity with the terrestrial bacteria Streptomyces lavendulae; however, they possess a greater secondary metabolite potential as estimated by the total number of identified biosynthetic gene clusters (BGCs). In particular, ICC1 and ICC4 had a greater number of polyketide and non-ribosomal peptide BGCs. The most frequently detected BGCs were those predicted to generate terpenes, small and low complexity dipeptides and lipids. Spectral analysis clearly identified a number of diketopiperazine products through matched reference spectra for cyclo (Leu-Pro), cyclo (Pro-Val) and cyclo [(4-hydroxyPro)-Leu]. One of the terpenes gene clusters predicted by antiSMASH possesses a seven-gene pathway consistent with diazepinomicin biosynthesis. This molecule contains a very rare core structure and its BGC, to date, has only been identified from a single bacterial genome. The tetrapeptide siderophore coelichelin BGC was unambiguously identified in the genome, however, the metabolite could not be identified from the culture extracts. Two type III polyketides, 2′, 5′ – dimethoxyflavone and nordentatin, were identified from the UHPLC-HRMS data of the aqueous and n-butanolic fractions of Streptomyces sp. ICC1, respectively. A BGC likely encoding these metabolites was predicted in both genomes. The predicted similarities in molecule production and genome shared by these two strains could be an indicative of a cooperative mode of living in extreme habitats instead of a competitive one. This secondary metabolite potential may contribute to the fitness of ICC1 and ICC4 in the Iron Curtain Cave.

Cave Actinobacteria as Producers of Bioactive Metabolites

Recently, there is an urgent need for new drugs due to the emergence of drug resistant pathogenic microorganisms and new infectious diseases. Members of phylum Actinobacteria are promising source of bioactive compounds notably antibiotics. The search for such new compounds has shifted to extreme or underexplored environments to increase the possibility of discovery. Cave ecosystems have attracted interest of the research community because of their unique characteristics and the microbiome residing inside including actinobacteria. At the time of writing, 47 species in 30 genera of actinobacteria were reported from cave and cave related habitats. Novel and promising bioactive compounds have been isolated and characterized. This mini-review focuses on the diversity of cultivable actinobacteria in cave and cave-related environments, and their bioactive metabolites from 1999 to 2018.

Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea

Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.

Mining Actinomycetes for Novel Antibiotics in the Omics Era: Are We Ready to Exploit This New Paradigm?

The current spread of multi-drug resistance in a number of key pathogens and the lack of therapeutic solutions in development to address most of the emerging infections in the clinic that are difficult to treat have become major concerns. Microbial natural products represent one of the most important sources for the discovery of potential new antibiotics and actinomycetes have been one of the most relevant groups that are prolific producers of these bioactive compounds. Advances in genome sequencing and bioinformatic tools have collected a wealth of knowledge on the biosynthesis of these molecules. This has revealed the broad untapped biosynthetic diversity of actinomycetes, with large genomes and the capacity to produce more molecules than previously estimated, opening new opportunities to identify the novel classes of compounds that are awaiting to be discovered. Comparative genomics, metabolomics and proteomics and the development of new analysis and genetic engineering tools provide access to the integration of new knowledge and better understanding of the physiology of actinomycetes and their tight regulation of the production of natural products antibiotics. This new paradigm is fostering the development of new genomic-driven and culture-based strategies, which aims to deliver new chemical classes of antibiotics to be developed to the clinic and replenish the exhausted pipeline of drugs for fighting the progression of infection diseases in the near future.