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Microbial diversity

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https://www.readbyqxmd.com/read/28534987/high%C3%A2-throughput-sequencing-analyses-of-oral-microbial-diversity-in-healthy-people-and-patients-with-dental-caries-and-periodontal-disease
#1
Tingtao Chen, Yan Shi, Xiaolei Wang, Xin Wang, Fanjing Meng, Shaoguo Yang, Jian Yang, Hongbo Xin
Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high‑throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people...
May 17, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28534905/antimicrobial-peptide-inspired-nh125-analogues-bacterial-and-fungal-biofilm-eradicating-agents-and-rapid-killers-of-mrsa-persisters
#2
Akash Basak, Yasmeen Abouelhassan, Ran Zuo, Hussain Yousaf, Yousong Ding, Robert W Huigens
During microbial infection, antimicrobial peptides are utilized by the immune response to rapidly eradicate microbial pathogens through the destruction of cellular membranes. Inspired by antimicrobial peptides, quaternary ammonium cationic (QAC) compounds have emerged as agents capable of destroying bacterial membranes leading to rapid bacterial death, including the eradication of persistent, surface-attached bacterial biofilms. NH125, an imidazolium cation with a sixteen membered fatty tail, was recently reported to eradicate persister cells and was our starting point for the development of novel antimicrobial agents...
May 23, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28534878/successive-range-expansion-promotes-diversity-and-accelerates-evolution-in-spatially-structured-microbial-populations
#3
Felix Goldschmidt, Roland R Regoes, David R Johnson
Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28533949/worldwide-exploration-of-the-microbiome-harbored-by-the-cnidarian-model-exaiptasia-pallida-agassiz-in-verrill-1864-indicates-a-lack-of-bacterial-association-specificity-at-a-lower-taxonomic-rank
#4
Tanya Brown, Christopher Otero, Alejandro Grajales, Estefania Rodriguez, Mauricio Rodriguez-Lanetty
Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community...
2017: PeerJ
https://www.readbyqxmd.com/read/28533782/towards-an-integrative-understanding-of-diet-host-gut-microbiome-interactions
#5
Mark N Read, Andrew J Holmes
Over the last 20 years, a sizeable body of research has linked the microbiome and host diet to a remarkable diversity of diseases. Yet, unifying principles of microbiome assembly or function, at levels required to rationally manipulate a specific individual's microbiome to their benefit, have not emerged. A key driver of both community composition and activity is the host diet, but diet-microbiome interactions cannot be characterized without consideration of host-diet interactions such as appetite and digestion...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28533770/from-vineyard-soil-to-wine-fermentation-microbiome-approximations-to-explain-the-terroir-concept
#6
REVIEW
Ignacio Belda, Iratxe Zarraonaindia, Matthew Perisin, Antonio Palacios, Alberto Acedo
Wine originally emerged as a serendipitous mix of chemistry and biology, where microorganisms played a decisive role. From these ancient fermentations to the current monitored industrial processes, winegrowers and winemakers have been continuously changing their practices according to scientific knowledge and advances. A new enology direction is emerging and aiming to blend the complexity of spontaneous fermentations with industrial safety of monitored fermentations. In this context, wines with distinctive autochthonous peculiarities have a great acceptance among consumers, causing important economic returns...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533768/novel-large-sulfur-bacteria-in-the-metagenomes-of-groundwater-fed-chemosynthetic-microbial-mats-in-the-lake-huron-basin
#7
Allison M Sharrar, Beverly E Flood, Jake V Bailey, Daniel S Jones, Bopaiah A Biddanda, Steven A Ruberg, Daniel N Marcus, Gregory J Dick
Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533766/predicting-the-hma-lma-status-in-marine-sponges-by-machine-learning
#8
Lucas Moitinho-Silva, Georg Steinert, Shaun Nielsen, Cristiane C P Hardoim, Yu-Chen Wu, Grace P McCormack, Susanna López-Legentil, Roman Marchant, Nicole Webster, Torsten Thomas, Ute Hentschel
The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533367/data-driven-modeling-reveals-cell-behaviors-controlling-self-organization-during-myxococcus-xanthus-development
#9
Christopher R Cotter, Heinz-Bernd Schüttler, Oleg A Igoshin, Lawrence J Shimkets
Collective cell movement is critical to the emergent properties of many multicellular systems, including microbial self-organization in biofilms, embryogenesis, wound healing, and cancer metastasis. However, even the best-studied systems lack a complete picture of how diverse physical and chemical cues act upon individual cells to ensure coordinated multicellular behavior. Known for its social developmental cycle, the bacterium Myxococcus xanthus uses coordinated movement to generate three-dimensional aggregates called fruiting bodies...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28533216/a-diverse-community-to-study-communities-integration-of-experiments-and-mathematical-models-to-study-microbial-consortia
#10
Antonella Succurro, Fiona Wanjiku Moejes, Oliver Ebenhöh
The last few years have seen the advancement of high-throughput experimental techniques produce an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from e.g. sequencing data, and often motivate further targeted experiments. The broad discipline of "computational biology" spans far beyond the well-established field of bioinformatics, but it is our impression that more theoretical methods like mathematical models are not yet as well integrated in the research studying microbial interactions...
May 22, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28531947/shifts-in-the-relative-abundance-of-bacteria-after-wine-lees-derived-biochar-intervention-in-multi-metal-contaminated-paddy-soil
#11
Min Xu, Hongxia Xia, Jun Wu, Gang Yang, Xiaohong Zhang, Hong Peng, Xiaoyu Yu, Li Li, Hong Xiao, Hui Qi
The impact of biochar application on soil ecological functions depends on the diversity of soil conditions and of the feedstocks from which biochar is obtained. Moreover, little information is available on the effect of biochar on dynamic changes in microorganisms with the development of rice plants in multi-metal-contaminated paddy soil amended with wine-lees-derived biochar. In this paper, biochar obtained from the pyrolysis of wine lees at 600°C was used to investigate the potential role of biochar in maintaining soil ecological functions, with consideration of the alteration of the microbial population over periods of rice growth...
May 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28531262/biogeography-of-cryoconite-bacterial-communities-on-glaciers-of-the-tibetan-plateau
#12
Yongqin Liu, Trista J Vick-Majors, John C Priscu, Tandong Yao, Shichang Kang, Keshao Liu, Ziyuang Cong, Jingbo Xiong, Yang Li
Cryoconite holes, water-filled pockets containing biological and mineralogical deposits that form on glacier surfaces, play important roles in glacier mass balance, glacial geochemistry, and carbon cycling. The presence of cryoconite material decreases surface albedo and accelerates glacier mass loss, a problem of particular importance in the rapidly melting Tibetan Plateau. No studies have addressed the microbial community composition of cryoconite holes and their associated ecosystem processes on Tibetan glaciers...
May 20, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28531216/impact-of-mutations-in-toll-like-receptor-pathway-genes-on-esophageal-carcinogenesis
#13
Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O'Donovan, Nick J Gay, Rebecca C Fitzgerald
Esophageal adenocarcinoma (EAC) develops in an inflammatory microenvironment with reduced microbial diversity, but mechanisms for these influences remain poorly characterized. We hypothesized that mutations targeting the Toll-like receptor (TLR) pathway could disrupt innate immune signaling and promote a microenvironment that favors tumorigenesis. Through interrogating whole genome sequencing data from 171 EAC patients, we showed that non-synonymous mutations collectively affect the TLR pathway in 25/171 (14...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28531174/genome-partitioner-a-web-tool-for-multi-level-partitioning-of-large-scale-dna-constructs-for-synthetic-biology-applications
#14
Matthias Christen, Luca Del Medico, Heinz Christen, Beat Christen
Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs...
2017: PloS One
https://www.readbyqxmd.com/read/28528783/revelation-and-cloning-of-valinomycin-synthetase-genes-in-streptomyces-lavendulae-acr-da1-and-their-expression-analysis-under-different-fermentation-and-elicitation-conditions
#15
Richa Sharma, Vijaylakshmi Jamwal, Varun P Singh, Priya Wazir, Praveen Awasthi, Deepika Singh, Sumit G Gandhi, Ram A Vishwakarma, Asha Chaubey
Streptomyces species are amongst the most exploited microorganisms due to their ability to produce a plethora of secondary metabolites with bioactive potential, including several well known drugs. They are endowed with immense unexplored potential and substantial efforts are required for their isolation as well as characterization for their bioactive potential. Unexplored niches and extreme environments are host to diverse microbial species. In this study, we report Streptomyces lavendulae ACR-DA1, isolated from extreme cold deserts of the North Western Himalayas, which produces a macrolactone antibiotic, valinomycin...
May 18, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28528651/manganese-in-marine-microbiology
#16
Colleen M Hansel
The importance of manganese in the physiology of marine microbes, the biogeochemistry of the ocean and the health of microbial communities of past and present is emerging. Manganese is distributed widely throughout the global ocean, taking the form of an essential antioxidant (Mn(2+)), a potent oxidant (Mn(3+)) and strong adsorbent (Mn oxides) sequestering disproportionately high levels of trace metals and nutrients in comparison to the surrounding seawater. Manganese is, in fact, linked to nearly all other elemental cycles and intricately involved in the health, metabolism and function of the ocean's microbiome...
2017: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/28528426/building-a-bio-based-industry-in-the-middle-east-through-harnessing-the-potential-of-the-red-sea-biodiversity
#17
REVIEW
Jens Nielsen, John Archer, Magbubah Essack, Vladimir B Bajic, Takashi Gojobori, Ivan Mijakovic
The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger "catalog" of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity...
May 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28527917/spatial-distribution-of-vanadium-and-microbial-community-responses-in-surface-soil-of-panzhihua-mining-and-smelting-area-china
#18
Xuelong Cao, Muhe Diao, Baogang Zhang, Hui Liu, Song Wang, Meng Yang
Spatial distribution of vanadium in surface soils from different processing stages of vanadium-bearing titanomagnetite in Panzhihua mining and smelting area (China) as well as responses of microbial communities including bacteria and fungi to vanadium were investigated by fieldwork and laboratory incubation experiment. The vanadium contents in this region ranged from 149.3 to 4793.6 mg kg(-1), exceeding the soil background value of vanadium in China (82 mg kg(-1)) largely. High-throughput DNA sequencing results showed bacterial communities from different manufacturing locations were quite diverse, but Bacteroidetes and Proteobacteria were abundant in all samples...
May 17, 2017: Chemosphere
https://www.readbyqxmd.com/read/28527760/restoration-of-cefixime-induced-gut-microbiota-changes-by-lactobacillus-cocktails-and-fructooligosaccharides-in-a-mouse-model
#19
Ying Shi, Qixiao Zhai, Dongyao Li, Bingyong Mao, Xiaoming Liu, Jianxin Zhao, Hao Zhang, Wei Chen
Probiotics have been used to rebuild the antibiotic-induced dysfunction in gut microbiota, but whether the different strains of probiotics result in similar or reverse effects remains unclear. In this study, the different recovery effects of two cocktails (each contains four strains) of Lactobacillus and fructooligosaccharide against cefixime-induced change of gut microbiota were evaluated in C57BL/6J mice. The results show that the use of cefixime caused a reduction in the diversities of the microbial community and led to significantly decreasing to one preponderant Firmicutes phylum, which was difficult to restore naturally in the short term...
July 2017: Microbiological Research
https://www.readbyqxmd.com/read/28527363/postmortem-microbial-communities-in-burial-soil-layers-of-skeletonized-humans
#20
Torri B Thomas, Sheree J Finley, Jeremy E Wilkinson, Daniel J Wescott, Azriel Gorski, Gulnaz T Javan
Microorganisms are major ecological participants in the successional decomposition of vertebrates. The relative abundance, or the scarcity, of certain microbial taxa in gravesoil has the potential to determine the ecological status of skeletons. However, there are substantial knowledge gaps that warrant consideration in the context of the surrounding terrestrial ecosystem. In the current study, we hypothesized that i.) soil microbial diversity is disparate in the latter stage of decomposition (skeletonization) compared to the earlier stages (fresh, bloat, active and advanced decay), and ii...
May 3, 2017: Journal of Forensic and Legal Medicine
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