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https://www.readbyqxmd.com/read/29651464/hex-a-heterologous-expression-platform-for-the-discovery-of-fungal-natural-products
#1
Colin J B Harvey, Mancheng Tang, Ulrich Schlecht, Joe Horecka, Curt R Fischer, Hsiao-Ching Lin, Jian Li, Brian Naughton, James Cherry, Molly Miranda, Yong Fuga Li, Angela M Chu, James R Hennessy, Gergana A Vandova, Diane Inglis, Raeka S Aiyar, Lars M Steinmetz, Ronald W Davis, Marnix H Medema, Elizabeth Sattely, Chaitan Khosla, Robert P St Onge, Yi Tang, Maureen E Hillenmeyer
For decades, fungi have been a source of U.S. Food and Drug Administration-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae ...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29610942/cross-reactivity-of-prokaryotic-16s-rdna-specific-primers-to-eukaryotic-dna-mistaken-microbial-community-profiling-in-environmental-samples
#2
Shailendra Yadav, Arvind Kumar, Manish Gupta, S S Maitra
16S ribosomal RNA gene sequences are characteristically used as gold-standard genetic marker for the determination of bacterial and/or archaeal biodiversity, and community profiling of environmental samples. The 16S rRNA amplicon analysis till-date is taken as a standard method for investigation and identification of uncultivable bacteria in microbial diversity studies. The accuracy of these analyses strongly depends upon the choice of primers. It is presumed that these primers do not participate in non-specific amplifications...
April 2, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29581530/genomic-expansion-of-magnetotactic-bacteria-reveals-an-early-common-origin-of-magnetotaxis-with-lineage-specific-evolution
#3
Wei Lin, Wensi Zhang, Xiang Zhao, Andrew P Roberts, Greig A Paterson, Dennis A Bazylinski, Yongxin Pan
The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3 O4 ) or greigite (Fe3 S4 ) called magnetosomes...
March 26, 2018: ISME Journal
https://www.readbyqxmd.com/read/29578082/genetics-of-human-and-animal-uncultivable-treponemal-pathogens
#4
REVIEW
David Šmajs, Michal Strouhal, Sascha Knauf
Treponema pallidum is an uncultivable bacterium and the causative agent of syphilis (subsp. pallidum [TPA]), human yaws (subsp. pertenue [TPE]), and bejel (subsp. endemicum). Several species of nonhuman primates in Africa are infected by treponemes genetically undistinguishable from known human TPE strains. Besides Treponema pallidum, the equally uncultivable Treponema carateum causes pinta in humans. In lagomorphs, Treponema paraluisleporidarum ecovar Cuniculus and ecovar Lepus are the causative agents of rabbit and hare syphilis, respectively...
March 22, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29575448/comparison-of-closely-related-uncultivated-coxiella-tick-endosymbiont-population-genomes-reveals-clues-about-the-mechanisms-of-symbiosis
#5
Despina Tsementzi, Juan Castro Gordillo, Mustafa Mahagna, Yuval Gottlieb, Konstantinos T Konstantinidis
Understanding the symbiotic interaction between Coxiella-like endosymbionts (CLE) and their tick hosts is challenging due to lack of isolates and difficulties in tick functional assays. Here we sequenced the metagenome of a CLE population from wild Rhipicephalus sanguineus ticks (CRs) and compared it to the previously published genome of its close relative, CLE of R. turanicus (CRt). The tick hosts are closely related sympatric species, and their two endosymbiont genomes are highly similar with only minor differences in gene content...
March 24, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29572583/insights-into-the-human-oral-microbiome
#6
REVIEW
Digvijay Verma, Pankaj Kumar Garg, Ashok Kumar Dubey
Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz...
March 23, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29559567/-in-vitro-culture-of-the-insect-endosymbiont-spiroplasma-poulsonii-highlights-bacterial-genes-involved-in-host-symbiont-interaction
#7
Florent Masson, Sandra Calderon Copete, Fanny Schüpfer, Gonzalo Garcia-Arraez, Bruno Lemaitre
Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongly affects its host's physiology, for example by causing male killing or by protecting it against various parasites...
March 20, 2018: MBio
https://www.readbyqxmd.com/read/29556819/phylogenetic-framework-for-the-phylum-tenericutes-based-on-genome-sequence-data-proposal-for-the-creation-of-a-new-order-mycoplasmoidales-ord-nov-containing-two-new-families-mycoplasmoidaceae-fam-nov-and-metamycoplasmataceae-fam-nov-harbouring-eperythrozoon
#8
Radhey S Gupta, Sahil Sawnani, Mobolaji Adeolu, Seema Alnajar, Aharon Oren
The genus Mycoplasma, including species earlier classified in the genera Eperythrozoon and Haemobartonella, contains ~ 120 species and constitutes an extensively polyphyletic assemblage of bacteria within the phylum Tenericutes. Due to their small genome sizes and lack of unique characteristics, the relationships among the mycoplasmas/Tenericutes are not reliably discerned. Using genome sequences for 140 Tenericutes, their evolutionary relationships were examined using multiple independent approaches. Phylogenomic trees were constructed for 63 conserved proteins, 45 ribosomal proteins, three main subunits of RNA polymerase and 16S rRNA gene sequences...
March 20, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29556533/it-takes-a-village-microbial-communities-thrive-through-interactions-and-metabolic-handoffs
#9
Laura A Hug, Rebecca Co
An enduring theme in microbial ecology is the interdependence of microbial community members. Interactions between community members include provision of cofactors, establishment of redox gradients, and turnover of key nutrients to drive biogeochemical cycles. Pathways canonically conducted by isolated organisms in laboratory cultures are instead collective products of diverse and interchangeable microbes in the environment. Current sequence-based methods provide unprecedented access to uncultivated microorganisms, allowing prediction of previously cryptic roles in biogeochemical cycles and interactions within communities...
March 2018: MSystems
https://www.readbyqxmd.com/read/29532802/in-situ-cultivation-of-previously-uncultivable-microorganisms-using-the-ichip
#10
Brittany Berdy, Amy L Spoering, Losee L Ling, Slava S Epstein
Most microbial species remain uncultivated, and modifying artificial nutrient media brings only an incremental increase in cultivability. We reasoned that an alternative way to cultivate species with unknown requirements is to use naturally occurring combinations of growth factors. To achieve this, we moved cultivation into the microbes' natural habitat by placing cells taken from varying environmental samples into diffusion chambers, which are then returned to nature for incubation. By miniaturizing the chambers and placing only one to several cells into each chamber, we can grow and isolate microorganisms in axenic culture in one step...
October 2017: Nature Protocols
https://www.readbyqxmd.com/read/29492594/a-crispy-diet-grazers-of-achromatium-oxaliferum-in-lake-stechlin-sediments
#11
Sina Schorn, Heribert Cypionka
Achromatium is the largest freshwater bacterium known to date and easily recognised by conspicuous calcite bodies filling the cell volume. Members of this genus are highly abundant in diverse aquatic sediments and may account for up to 90% of the bacterial biovolume in the oxic-anoxic interfaces. The high abundance implies that Achromatium is either rapidly growing or hardly prone to predation. As Achromatium is still uncultivated and does not appear to grow fast, one could assume that the cells might escape predation by their unusual shape and composition...
February 28, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29490697/-candidatus-paraporphyromonas-polyenzymogenes-encodes-multi-modular-cellulases-linked-to-the-type-ix-secretion-system
#12
A E Naas, L M Solden, A D Norbeck, H Brewer, L H Hagen, I M Heggenes, A C McHardy, R I Mackie, L Paša-Tolić, M Ø Arntzen, V G H Eijsink, N M Koropatkin, M Hess, K C Wrighton, P B Pope
BACKGROUND: In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa...
March 1, 2018: Microbiome
https://www.readbyqxmd.com/read/29483268/transitory-microbial-habitat-in-the-hyperarid-atacama-desert
#13
Dirk Schulze-Makuch, Dirk Wagner, Samuel P Kounaves, Kai Mangelsdorf, Kevin G Devine, Jean-Pierre de Vera, Philippe Schmitt-Kopplin, Hans-Peter Grossart, Victor Parro, Martin Kaupenjohann, Albert Galy, Beate Schneider, Alessandro Airo, Jan Frösler, Alfonso F Davila, Felix L Arens, Luis Cáceres, Francisco Solís Cornejo, Daniel Carrizo, Lewis Dartnell, Jocelyne DiRuggiero, Markus Flury, Lars Ganzert, Mark O Gessner, Peter Grathwohl, Lisa Guan, Jacob Heinz, Matthias Hess, Frank Keppler, Deborah Maus, Christopher P McKay, Rainer U Meckenstock, Wren Montgomery, Elizabeth A Oberlin, Alexander J Probst, Johan S Sáenz, Tobias Sattler, Janosch Schirmack, Mark A Sephton, Michael Schloter, Jenny Uhl, Bernardita Valenzuela, Gisle Vestergaard, Lars Wörmer, Pedro Zamorano
Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth...
March 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29476141/genome-resolved-metagenomics-identifies-genetic-mobility-metabolic-interactions-and-unexpected-diversity-in-perchlorate-reducing-communities
#14
Tyler P Barnum, Israel A Figueroa, Charlotte I Carlström, Lauren N Lucas, Anna L Engelbrektson, John D Coates
Dissimilatory perchlorate reduction is an anaerobic respiratory pathway that in communities might be influenced by metabolic interactions. Because the genes for perchlorate reduction are horizontally transferred, previous studies have been unable to identify uncultivated perchlorate-reducing populations. Here we recovered metagenome-assembled genomes from perchlorate-reducing sediment enrichments and employed a manual scaffolding approach to reconstruct gene clusters for perchlorate reduction found within mobile genetic elements...
February 23, 2018: ISME Journal
https://www.readbyqxmd.com/read/29475572/abditibacterium-utsteinense-sp-nov-the-first-cultivated-member-of-candidate-phylum-fbp-isolated-from-ice-free-antarctic-soil-samples
#15
Guillaume Tahon, Bjorn Tytgat, Liesbeth Lebbe, Aurélien Carlier, Anne Willems
Most bacterial lineages are known only by molecular sequence data from environmental surveys and represent the uncultivated majority. One of these lineages, candidate phylum FBP, is widespread in extreme environments on Earth, ranging from polar and desert ecosystems to wastewater and contaminated mine sites. Here we report on the characterization of strain LMG 29911T , the first cultivated representative of the FBP lineage. The strain was isolated from a terrestrial surface sample from Utsteinen, Sør Rondane Mountains, East Antarctica and is a Gram-negative, aerobic, oligotrophic chemoheterotrophic bacterium...
February 7, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29467733/diversity-of-rare-and-abundant-prokaryotic-phylotypes-in-the-prony-hydrothermal-field-and-comparison-with-other-serpentinite-hosted-ecosystems
#16
Eléonore Frouin, Méline Bes, Bernard Ollivier, Marianne Quéméneur, Anne Postec, Didier Debroas, Fabrice Armougom, Gaël Erauso
The Bay of Prony, South of New Caledonia, represents a unique serpentinite-hosted hydrothermal field due to its coastal situation. It harbors both submarine and intertidal active sites, discharging hydrogen- and methane-rich alkaline fluids of low salinity and mild temperature through porous carbonate edifices. In this study, we have extensively investigated the bacterial and archaeal communities inhabiting the hydrothermal chimneys from one intertidal and three submarine sites by 16S rRNA gene amplicon sequencing...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29463892/microbial-cycling-of-isoprene-the-most-abundantly-produced-biological-volatile-organic-compound-on-earth
#17
Terry J McGenity, Andrew T Crombie, J Colin Murrell
Isoprene (2-methyl-1,3-butadiene), the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, is highly reactive and can have diverse and often detrimental atmospheric effects, which impact on climate and health. Most isoprene is produced by terrestrial plants, but (micro)algal production is important in aquatic environments, and the relative bacterial contribution remains unknown. Soils are a sink for isoprene, and bacteria that can use isoprene as a carbon and energy source have been cultivated and also identified using cultivation-independent methods from soils, leaves and coastal/marine environments...
February 20, 2018: ISME Journal
https://www.readbyqxmd.com/read/29463658/functional-and-expression-analyses-of-the-pneumocystis-mat-genes-suggest-obligate-sexuality-through-primary-homothallism-within-host-lungs
#18
S Richard, J M G C F Almeida, O H Cissé, A Luraschi, O Nielsen, M Pagni, P M Hauser
Fungi of the genus Pneumocystis are obligate parasites that colonize mammals' lungs and are host species specific. Pneumocystis jirovecii and Pneumocystis carinii infect, respectively, humans and rats. They can turn into opportunistic pathogens in immunosuppressed hosts, causing severe pneumonia. Their cell cycle is poorly known, mainly because of the absence of an established method of culture in vitro It is thought to include both asexual and sexual phases. Comparative genomic analysis suggested that their mode of sexual reproduction is primary homothallism involving a single mating type ( MAT ) locus encompassing plus and minus genes ( matMc , matMi , and matPi ; Almeida et al...
February 20, 2018: MBio
https://www.readbyqxmd.com/read/29462300/dna-stable-isotope-probing-identifies-uncultivated-members-of-pseudonocardia-associated-with-biodegradation-of-pyrene-in-agricultural-soil
#19
Song-Can Chen, Gui-Lan Duan, Kai Ding, Fu-Yi Huang, Yong-Guan Zhu
Identifying functional microorganisms involved in the degradation of high-molecular-mass polycyclic aromatic hydrocarbons (HMM-PAHs) in agricultural soil environments could assist in developing bioremediation strategies for soil PAH-contamination. Active populations of HMM-PAHs degraders in agricultural soils are currently poorly understood. In this study, we identified aerobic pyrene-degrading bacteria in agricultural and industrial soils by 13C-pyrene incubations followed by DNA stable isotope probing (DNA-SIP) and high-throughput sequencing...
February 15, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29460534/focus-on-periodontal-disease-and-development-of-endocarditis
#20
F Carinci, M Martinelli, M Contaldo, R Santoro, F Pezzetti, D Lauritano, V Candotto, D Mucchi, A Palmieri, A Tagliabue, L Tettamanti
Infective endocarditis is a devastating disease with high morbidity and mortality. The link to oral bacteria has been known for many decades and has caused ongoing concern for dentists, patients and cardiologists. The microbiota of the mouth is extremely diverse and more than 700 bacterial species have been detected. Half of them are uncultivable so far. Oral microbiota is not uniform, specific sites exist in the mouth such as tongue, palate, cheek, teeth and periodontal pockets that have their own microbiota...
January 2018: Journal of Biological Regulators and Homeostatic Agents
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