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https://www.readbyqxmd.com/read/28717356/thermoplasmatales-and-methanogens-potential-association-with-the-crenarchaeol-production-in-chinese-soils
#1
Fuyan Li, Fengfeng Zheng, Yongli Wang, Weiguo Liu, Chuanlun L Zhang
Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28716079/the-human-jejunum-has-an-endogenous-microbiota-that-differs-from-those-in-the-oral-cavity-and-colon
#2
Olof H Sundin, Antonio Mendoza-Ladd, Mingtao Zeng, Diana Diaz-Arévalo, Elisa Morales, B Matthew Fagan, Javier Ordoñez, Philip Velez, Nishaal Antony, Richard W McCallum
BACKGROUND: The upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 10(11)-10(12) colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 10(3) to 10(5) CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics...
July 17, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28709072/stimulation-effect-of-electric-current-density-ecd-on-microbial-community-of-a-three-dimensional-particle-electrode-coupled-with-biological-aerated-filter-reactor-tde-baf
#3
Yan Feng, Xing Li, Ting Song, Yanzhen Yu, Jingyao Qi
Improving the stimulation effect of electric current density (ECD) on microbial community is critical in designing and operating TDE-BAF. This study investigated the effect of ECD at 0.00, 4.08, 6.12, 12.20, 14.25, 16.30 and 20.20A·m(-2) on the removal performance, diversity and structure of microbial community in TDE-BAF. Results indicated that the ECD of 14.25A·m(-2) exhibited the highest COD, TOC and NH4(+)-N average removal rates with 93.33%, 91.26% and 93.87%, respectively; Under high ECD, especially exceeding 14...
July 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28701744/massively-parallel-whole-genome-amplification-for-single-cell-sequencing-using-droplet-microfluidics
#4
Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama
Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28697806/control-of-lupus-nephritis-by-changes-of-gut-microbiota
#5
Qinghui Mu, Husen Zhang, Xiaofeng Liao, Kaisen Lin, Hualan Liu, Michael R Edwards, S Ansar Ahmed, Ruoxi Yuan, Liwu Li, Thomas E Cecere, David B Branson, Jay L Kirby, Poorna Goswami, Caroline M Leeth, Kaitlin A Read, Kenneth J Oestreich, Miranda D Vieson, Christopher M Reilly, Xin M Luo
BACKGROUND: Systemic lupus erythematosus, characterized by persistent inflammation, is a complex autoimmune disorder with no known cure. Immunosuppressants used in treatment put patients at a higher risk of infections. New knowledge of disease modulators, such as symbiotic bacteria, can enable fine-tuning of parts of the immune system, rather than suppressing it altogether. RESULTS: Dysbiosis of gut microbiota promotes autoimmune disorders that damage extraintestinal organs...
July 11, 2017: Microbiome
https://www.readbyqxmd.com/read/28697453/electricity-production-and-microbial-characterization-of-thermophilic-microbial-fuel-cells
#6
Kun Dai, Jun-Li Wen, Fang Zhang, Xi-Wen Ma, Xiang-Yu Cui, Qi Zhang, Ting-Jia Zhao, Raymond J Zeng
Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m(2), and the columbic efficiency in this work was 20...
July 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28695385/recovery-of-previously-uncultured-bacterial-genera-from-three-mediterranean-sponges
#7
Dennis Versluis, Kyle McPherson, Mark W J van Passel, Hauke Smidt, Detmer Sipkema
Sponges often harbour a dense and diverse microbial community. Presently, a large discrepancy exists between the cultivable bacterial fraction from sponges and the community in its natural environment. Here, we aimed to acquire additional insights into cultivability of (previously uncultured) bacteria from three sponge species, namely Aplysina aerophoba, Corticium candelabrum and Petrosia ficiformis, by studying bacterial growth on five media in the form of 60 communities scraped from plates without antibiotics, as well as in the form of individual isolates that were grown on these media supplemented with antibiotics...
July 10, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28693474/assembling-metagenomes-one-community-at-a-time
#8
Andries Johannes van der Walt, Marc Warwick van Goethem, Jean-Baptiste Ramond, Thulani Peter Makhalanyane, Oleg Reva, Don Arthur Cowan
BACKGROUND: Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data. RESULTS: To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets...
July 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28690595/culture-independent-analyses-reveal-novel-anaerolineaceae-as-abundant-primary-fermenters-in-anaerobic-digesters-treating-waste-activated-sludge
#9
Simon J McIlroy, Rasmus H Kirkegaard, Morten S Dueholm, Eustace Fernando, Søren M Karst, Mads Albertsen, Per H Nielsen
Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp) from a representative of the A6 taxon...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28687857/improving-catalytic-performance-of-an-arylacetonitrilase-by-semirational-engineering
#10
Ya-Ping Xue, Biao Jiao, Deng-En Hua, Feng Cheng, Zhi-Qiang Liu, Yu-Guo Zheng
Arylacetonitrilases have been widely acknowledged as important alternatives to chemical catalysts for synthesizing optically pure 2-hydroxyphenylacetic acids from nitriles. In this work, two residues (Thr132 and Ser190) located at the catalytic tunnel in the active site of an arylacetonitrilase nitA from uncultured organisms were mutated separately by site-directed mutagenesis. Ser190 was demonstrated to be the critical position which has a greater influence on arylacetonitrilase nitA activity than Thr132. The replacement of serine at position 190 with glycine increases its activity toward mandelonitrile and (o, m, p)-chloromandelonitrile, whereas replacing it with leucine abolished its activity...
July 7, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/28686606/plant-fed-versus-chemicals-fed-rhizobacteria-of-lucerne-plant-only-teabags-culture-media-not-only-increase-culturability-of-rhizobacteria-but-also-recover-a-previously-uncultured-lysobacter-sp-novosphingobium-sp-and-pedobacter-sp
#11
Nabil A Hegazi, Mohamed S Sarhan, Mohamed Fayez, Sascha Patz, Brian R Murphy, Silke Ruppel
In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR)...
2017: PloS One
https://www.readbyqxmd.com/read/28680072/-arman-archaea-depend-on-association-with-euryarchaeal-host-in-culture-and-in-situ
#12
Olga V Golyshina, Stepan V Toshchakov, Kira S Makarova, Sergey N Gavrilov, Aleksei A Korzhenkov, Violetta La Cono, Erika Arcadi, Taras Y Nechitaylo, Manuel Ferrer, Ilya V Kublanov, Yuri I Wolf, Michail M Yakimov, Peter N Golyshin
Intriguing, yet uncultured 'ARMAN'-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0...
July 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28647881/alterations-in-soil-microbial-communities-caused-by-treatments-with-penicillin-or-neomycin
#13
Qichun Zhang, Ouyang Kang, Salma Jabeen, Warren A Dick
Antibiotic residues in soils can lead to serious health risk and ecological hazards. In this study, the effects of penicillin and neomycin, two antibiotics widely used in animal production, were investigated on soil bacterial communities. Changes in the community structure were monitored using three 16S ribosomal DNA (rDNA) polymerase chain reaction-based approaches, including denaturing gradient gel electrophoresis (DGGE), amplified rDNA restriction analysis (ARDRA), and terminal-restriction fragment length polymorphism (T-RFLP) analysis...
June 25, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28646115/genome-analysis-of-endomicrobium-proavitum-suggests-loss-and-gain-of-relevant-functions-during-the-evolution-of-intracellular-symbionts
#14
Hao Zheng, Carsten Dietrich, Andreas Brune
Bacterial endosymbionts of eukaryotes show progressive genome erosion, but detailed investigations of the evolutionary processes involved in the transition to an intracellular lifestyle are generally hampered by the lack of extant free-living lineages. Here, we characterize the genome of the recently isolated, free-living Endomicrobium proavitum, the second member of the Elusimicrobia phylum brought into pure culture, and compare it to the closely related "Candidatus Endomicrobium trichonymphae" strain Rs-D17, a previously described but uncultured endosymbiont of termite gut flagellates...
June 23, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28645159/genomic-characterization-of-two-novel-sar11-isolates-from-the-red-sea-including-the-first-strain-of-the-sar11-ib-clade
#15
Francy Jimenez-Infante, David Kamanda Ngugi, Manikandan Vinu, Jochen Blom, Intikhab Alam, Vladimir B Bajic, Ulrich Stingl
The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28629639/atp-synthesis-capacity-of-pulsed-light-exposed-bacteria
#16
B Kramer, J Wunderlich, P Muranyi
The ability of four different bacteria to synthesize new ATP upon exposure to different doses of pulsed-light (PL) irradiation was investigated. The bacterial cells were PL treated on a gel surface, resuspended in phosphate buffered saline (PBS) and subsequently incubated in Tryptic Soy Broth (TSB) at 37°C. Cellular ATP levels were monitored during a 2h incubation period and compared to the respective colony count data. Although PL affected ATP production in a dose dependent manner, the results showed that bacteria, which had rendered unculturable after PL exposure, are still capable of generating significant quantities of ATP...
June 7, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28629476/stromal-vascular-fraction-cells-for-the-treatment-of-critical-limb-ischemia-a-pilot-study
#17
Adas Darinskas, Mindaugas Paskevicius, Gintaras Apanavicius, Gintaris Vilkevicius, Liutauras Labanauskas, Thomas E Ichim, Rytis Rimdeika
BACKGROUND: Cell-based therapy is being explored as an alternative treatment option for critical limb ischemia (CLI), a disease associated with high amputation and mortality rates and poor quality of life. However, therapeutic potential of uncultured adipose-derived stromal vascular fraction (SVF) cells has not been evaluated as a possible treatment. In this pilot study, we investigated the efficacy of multiple injections of autologous uncultured adipose-derived SVF cells to treat patients with CLI...
June 19, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28628218/microbiota-analysis-using-an-illumina-miseq-platform-to-sequence-16s-rrna-genes
#18
Alexis Rapin, Céline Pattaroni, Benjamin J Marsland, Nicola L Harris
The microbiota have been shown to play an important role in diverse biological processes including immunity, metabolism, and digestion. Assessing the exact composition of the microbiota has proven challenging due to the often unknown growth specificities of its members, and culture-based approaches typically fail to capture the complete diversity of microorganisms present. Next Generation Sequencing (NGS) methods provide an efficient means to gather information about cultured and uncultured members of the microbiota...
June 19, 2017: Current Protocols in Mouse Biology
https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#19
Calvin Ho-Fung Lau, Kalene van Engelen, Stephen Gordon, Justin Renaud, Edward Topp
Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hotspots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28624689/from-complex-gut-communities-to-minimal-microbiomes-via-cultivation
#20
REVIEW
Thomas Clavel, Ilias Lagkouvardos, Bärbel Stecher
The mammalian gut microbiota is dominated by populations of bacteria, mostly strict anaerobes. Because these bacteria can influence the health of their host, it is important to investigate their diversity and functions, which can be done via culture-based or molecular approaches. In recent years, microbiologists have very often preferred the use of molecular techniques, as they do not limit the analysis to the fraction of communities that can be grown in the laboratory. In reality, cultivation and molecular methods are complementary, and we are now witnessing a period of unification...
June 15, 2017: Current Opinion in Microbiology
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