Cave Microbiomes: A Novel Resource for Drug Discovery

Cheeptham, Naowarat

doi:10.1007/978-1-4614-5206-5

Cited by 25 publications

(4 citation statements)

References 98 publications

(166 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A metagenomic approach is often used in order to understand better the biodiversity of microbiota present in a given habitat; it has evolved very quickly in the last years and is now largely focused on massive sequencing of DNA directly extracted from various environments. It represents an indispensable tool in many areas of research because it is now accepted that in most cases the behaviour of individual species can only be explained in a community context (Cheeptham, 2013).…”

Section: Introductionmentioning

confidence: 99%

Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies

Kraková

Leo

Bruno

et al. 2015

Environmental Microbiology

View full text Add to dashboard Cite

Roman Catacombs are affected by different kinds of biofilms that were extensively investigated in the last 14 years. In particular, the areas far from the lamps are often covered by white biofilms of different extension, consistency and nature. The aim of this paper is to describe the profile of the microbial community present in two areas of the Ocean's Cubiculum (CSC13), characterized by similar alterations described as white biofilms, by using a multistep approach that included direct microscopy observations, culture-dependent and culture-independent methodologies through the extraction of DNA and RNA directly from the sampled areas. In addition to this, we extracted the DNA directly from the Petri dishes containing R2A and B4 media after incubation and growth of bacteria. Our results evidenced that a complex bacterial community (mainly constituted by filamentous Actinobacteria, as well as Firmicutes and Proteobacteria) colonizes the two different white biofilms, and its detection, quantitative and qualitative, could be revealed only by different approaches, each method giving different information that only partially overlap.

show abstract

Section: Introductionmentioning

confidence: 99%

Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies

Kraková

Leo

Bruno

et al. 2015

Environmental Microbiology

View full text Add to dashboard Cite

show abstract

“…Deep biosphere Caves, mines, and other deep underground environments contain unique edaphic qualities and are often characterized by low nutrient availability, limited nutrient diversity, stable physical environments, low microbial biomass, low microbial diversity, high humidity, and high metal concentrations, [5,32]. They display increased stability to physical perturbations compared to terrestrial environments and less mixing than marine environments.…”

Section: Biogeography Of Microbial Nps: Habitat Variation and Spatialmentioning

confidence: 99%

Leveraging ecological theory to guide natural product discovery

Smanski

Schlatter

Kinkel

2016

Journal of Industrial Microbiology and Biotechnology

View full text Add to dashboard Cite

Technological improvements have accelerated natural product (NP) discovery and engineering to the point that systematic genome mining for new molecules is on the horizon. NP biosynthetic potential is not equally distributed across organisms, environments, or microbial life histories, but instead is enriched in a number of prolific clades. Also, NPs are not equally abundant in nature; some are quite common and others markedly rare. Armed with this knowledge, random 'fishing expeditions' for new NPs are increasingly harder to justify. Understanding the ecological and evolutionary pressures that drive the non-uniform distribution of NP biosynthesis provides a rational framework for the targeted isolation of strains enriched in new NP potential. Additionally, ecological theory leads to testable hypotheses regarding the roles of NPs in shaping ecosystems. Here we review several recent strain prioritization practices and discuss the ecological and evolutionary underpinnings for each. Finally, we offer perspectives on leveraging microbial ecology and evolutionary biology for future NP discovery.

show abstract

“…There are also reports on some species of the genus Agromyces taking part in plant xylems natural degradation [24] or sea food fermentation [25]. So far, strains of the genus Agromyces have not been described from a karst cave ecosystem, a nutrient-limited, redox-reaction-active habitat of high microbial diversity, which is predicted to be a treasure trove of new bacterial species [26]. During research on the actinobacterial diversity in a karst cave niche, several actinobacteria strains were isolated from a wet stone fragment sample from a typical karst cavernous wall surface in Lion Rock, a subtropical karst cave in Guangdong, PR China.…”

Section: Full-textmentioning

confidence: 99%

Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan

Fang

Gao

Jiao

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

A novel actinobacterial strain, designated SYSU K20354T, was isolated from a soil sample collected from a karst cave in Shaoguan city, Guangdong province, southern China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K20354T was most closely related to Agromyces humatus JCM 14319T, and shared the highest sequence identity of 98.3 % based on NCBI database. In addition, 2,4-diaminobutyric acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose and ribose. The major isoprenoid quinone was MK-12, while the major fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, three unknown glycolipids, three unknown phospholipids and two unknown lipids. The draft genome size of strain SYSU K20354T was 3.96 Mbp with G+C content of 69.7 mol%. Furthermore, the average nucleotide identity and digital DNA–DNA hybridization values between strain SYSU K20354T and A. humatus JCM 14319T were 90.3 and 55.6 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K20354T represents a novel species of the genus Agromyces , for which the name Agromyces cavernae sp. nov. is proposed. The type strain is SYSU K20354T (=KCTC 49499T= CGMCC 4.7691T).

show abstract

Cave Microbiomes: A Novel Resource for Drug Discovery

Cited by 25 publications

References 98 publications

Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies

Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies

Leveraging ecological theory to guide natural product discovery

Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan

Contact Info

Product

Resources

About