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https://www.readbyqxmd.com/read/29124129/subtle-microbiome-manipulation-using-probiotics-reduces-antibiotic-associated-mortality-in-fish
#1
Victor Schmidt, Marta Gomez-Chiarri, Chelsea Roy, Katherine Smith, Linda Amaral-Zettler
Prophylactic antibiotics in the aquaculture and ornamental fish industry are intended to prevent the negative impacts of disease outbreaks. Research in mice and humans suggests that antibiotics may disturb microbiome communities and decrease microbiome-mediated disease resistance, also known as "colonization resistance." If antibiotics impact fish as they do mice and humans, prophylactic administrations on aquaculture farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits...
November 2017: MSystems
https://www.readbyqxmd.com/read/29104938/vitamin-and-amino-acid-auxotrophy-in-anaerobic-consortia-operating-under-methanogenic-conditions
#2
Valerie Hubalek, Moritz Buck, BoonFei Tan, Julia Foght, Annelie Wendeberg, David Berry, Stefan Bertilsson, Alexander Eiler
Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions...
September 2017: MSystems
https://www.readbyqxmd.com/read/29085915/an-important-role-for-purifying-selection-in-archaeal-genome-evolution
#3
Zhe Lyu, Zhi-Gang Li, Fei He, Ziding Zhang
As the null hypothesis of genome evolution, population genetic theory suggests that selection strength controls genome size. Through the process of genetic drift, this theory predicts that compact genomes are maintained by strong purifying selection while complex genomes are enabled by weak purifying selection. It offers a unifying framework that explains why prokaryotic genomes are much smaller than their eukaryotic counterparts. However, recent findings suggest that bigger prokaryotic genomes appear to experience stronger purifying selection, indicating that purifying selection may not dominate prokaryotic genome evolution...
September 2017: MSystems
https://www.readbyqxmd.com/read/29085914/multi-omics-comparative-analysis-reveals-multiple-layers-of-host-signaling-pathway-regulation-by-the-gut-microbiota
#4
Nathan P Manes, Natalia Shulzhenko, Arthur G Nuccio, Sara Azeem, Andrey Morgun, Aleksandra Nita-Lazar
The bodies of mammals are hosts to vast microbial communities composed of trillions of bacteria from thousands of species, whose effects on health and development have begun to be appreciated only recently. In this investigation, an integrated analysis combining proteomics and transcriptomics was used to quantitatively compare the terminal ilia from conventional and germfree mice. Female and male mice responded similarly to the microbiota, but C57BL/10A mice responded more strongly than BALB/c mice at both the transcriptome and proteome levels...
September 2017: MSystems
https://www.readbyqxmd.com/read/29034331/extensive-core-microbiome-in-drone-captured-whale-blow-supports-a-framework-for-health-monitoring
#5
Amy Apprill, Carolyn A Miller, Michael J Moore, John W Durban, Holly Fearnbach, Lance G Barrett-Lennard
The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community...
September 2017: MSystems
https://www.readbyqxmd.com/read/29034330/perinatal-bisphenol-a-exposure-induces-chronic-inflammation-in-rabbit-offspring-via-modulation-of-gut-bacteria-and-their-metabolites
#6
Lavanya Reddivari, D N Rao Veeramachaneni, William A Walters, Catherine Lozupone, Jennifer Palmer, M K Kurundu Hewage, Rohil Bhatnagar, Amnon Amir, Mary J Kennett, Rob Knight, Jairam K P Vanamala
Bisphenol A (BPA) accumulates in the maturing gut and liver in utero and is known to alter gut bacterial profiles in offspring. Gut bacterial dysbiosis may contribute to chronic colonic and systemic inflammation. We hypothesized that perinatal BPA exposure-induced intestinal (and liver) inflammation in offspring is due to alterations in the microbiome and colonic metabolome. The 16S rRNA amplicon sequencing analysis revealed differences in beta diversity with a significant reduction in the relative abundances of short-chain fatty acid (SCFA) producers such as Oscillospira and Ruminococcaceae due to BPA exposure...
September 2017: MSystems
https://www.readbyqxmd.com/read/29034329/comparative-metabolomics-of-mycoplasma-bovis-and-mycoplasma-gallisepticum-reveals-fundamental-differences-in-active-metabolic-pathways-and-suggests-novel-gene-annotations
#7
Y Masukagami, D P De Souza, S Dayalan, C Bowen, S O'Callaghan, K Kouremenos, B Nijagal, D Tull, K A Tivendale, P F Markham, M J McConville, G F Browning, F M Sansom
Mycoplasmas are simple, but successful parasites that have the smallest genome of any free-living cell and are thought to have a highly streamlined cellular metabolism. Here, we have undertaken a detailed metabolomic analysis of two species, Mycoplasma bovis and Mycoplasma gallisepticum, which cause economically important diseases in cattle and poultry, respectively. Untargeted gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analyses of mycoplasma metabolite extracts revealed significant differences in the steady-state levels of many metabolites in central carbon metabolism, while (13)C stable isotope labeling studies revealed marked differences in carbon source utilization...
September 2017: MSystems
https://www.readbyqxmd.com/read/28951891/thiamine-acquisition-strategies-impact-metabolism-and-competition-in-the-gut-microbe-bacteroides-thetaiotaomicron
#8
Zachary A Costliow, Patrick H Degnan
Thiamine (vitamin B1) is an essential cofactor for all organisms. Humans primarily acquire thiamine through their diet, and thiamine deficiencies have adverse neurological effects. However, the role gut microbes play in modulating thiamine availability is poorly understood, and little is known about how thiamine impacts the stability of microbial gut communities. To investigate thiamine's role in the gut, we utilized the model gut microbe Bacteroides thetaiotaomicron. Transcriptome sequencing (RNA-seq) revealed a global downregulation of thiamine and amino acid biosynthesis, glycolysis, and purine metabolism when thiamine was present...
September 2017: MSystems
https://www.readbyqxmd.com/read/28951890/the-induction-of-oxalate-metabolism-in-vivo-is-more-effective-with-functional-microbial-communities-than-with-functional-microbial-species
#9
Aaron W Miller, Colin Dale, M Denise Dearing
For mammals, oxalate enters the body through the diet or is endogenously produced by the liver; it is removed by microbial oxalate metabolism in the gut and/or excretion in feces or urine. Deficiencies in any one of the these pathways can lead to complications, such as calcium oxalate urinary stones. While considerable research has been conducted on individual oxalate-degrading bacterial isolates, interactions between oxalate and the gut microbiota as a whole are unknown. We examined the reduction in oxalate excretion in a rat model following oral administration of fecal microbes from a mammalian herbivore adapted to a high oxalate diet or to fecal transplants consisting of two different formulations of mixed oxalate-degrading isolates...
September 2017: MSystems
https://www.readbyqxmd.com/read/28951889/functional-changes-in-the-gut-microbiome-contribute-to-transforming-growth-factor-%C3%AE-deficient-colon-cancer
#10
Scott G Daniel, Corbie L Ball, David G Besselsen, Tom Doetschman, Bonnie L Hurwitz
Colorectal cancer (CRC) is one of the most treatable cancers, with a 5-year survival rate of ~64%, yet over 50,000 deaths occur yearly in the United States. In 15% of cases, deficiency in mismatch repair leads to null mutations in transforming growth factor β (TGF-β) type II receptor, yet genotype alone is not responsible for tumorigenesis. Previous work in mice shows that disruptions in TGF-β signaling combined with Helicobacter hepaticus cause tumorigenesis, indicating a synergistic effect between genotype and microbial environment...
September 2017: MSystems
https://www.readbyqxmd.com/read/28951888/systematic-discovery-of-archaeal-transcription-factor-functions-in-regulatory-networks-through-quantitative-phenotyping-analysis
#11
Cynthia L Darnell, Peter D Tonner, Jordan G Gulli, Scott C Schmidler, Amy K Schmid
Gene regulatory networks (GRNs) are critical for dynamic transcriptional responses to environmental stress. However, the mechanisms by which GRN regulation adjusts physiology to enable stress survival remain unclear. Here we investigate the functions of transcription factors (TFs) within the global GRN of the stress-tolerant archaeal microorganism Halobacterium salinarum. We measured growth phenotypes of a panel of TF deletion mutants in high temporal resolution under heat shock, oxidative stress, and low-salinity conditions...
September 2017: MSystems
https://www.readbyqxmd.com/read/28951887/proteomes-of-lactobacillus-delbrueckii-subsp-bulgaricus-lbb-b5-incubated-in-milk-at-optimal-and-low-temperatures
#12
Xiaochen Yin, Michelle R Salemi, Brett S Phinney, Velitchka Gotcheva, Angel Angelov, Maria L Marco
We identified the proteins synthesized by Lactobacillus delbrueckii subsp. bulgaricus strain LBB.B5 in laboratory culture medium (MRS) at 37°C and milk at 37 and 4°C. Cell-associated proteins were measured by gel-free, shotgun proteomics using high-performance liquid chromatography coupled with tandem mass spectrophotometry. A total of 635 proteins were recovered from all cultures, among which 72 proteins were milk associated (unique or significantly more abundant in milk). LBB.B5 responded to milk by increasing the production of proteins required for purine biosynthesis, carbohydrate metabolism (LacZ and ManM), energy metabolism (TpiA, PgK, Eno, SdhA, and GapN), amino acid synthesis (MetE, CysK, LBU0412, and AspC) and transport (GlnM and GlnP), and stress response (Trx, MsrA, MecA, and SmpB)...
September 2017: MSystems
https://www.readbyqxmd.com/read/28905001/genome-enabled-insights-into-the-ecophysiology-of-the-comammox-bacterium-candidatus-nitrospira-nitrosa
#13
Pamela Y Camejo, Jorge Santo Domingo, Katherine D McMahon, Daniel R Noguera
The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions...
September 2017: MSystems
https://www.readbyqxmd.com/read/28905000/transcriptome-analysis-of-polyhydroxybutyrate-cycle-mutants-reveals-discrete-loci-connecting-nitrogen-utilization-and-carbon-storage-in-sinorhizobium-meliloti
#14
Maya D'Alessio, Ricardo Nordeste, Andrew C Doxey, Trevor C Charles
Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti, we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis (phbA, phbB, phbAB, and phbC), PHB degradation (bdhA, phaZ, and acsA2), and glycogen synthesis (glgA1)...
September 2017: MSystems
https://www.readbyqxmd.com/read/28904999/linking-spatial-structure-and-community-level-biotic-interactions-through-cooccurrence-and-time-series-modeling-of-the-human-intestinal-microbiota
#15
Eric J de Muinck, Knut E A Lundin, Pål Trosvik
The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract...
September 2017: MSystems
https://www.readbyqxmd.com/read/28904998/parallel-evolution-of-group-b-streptococcus-hypervirulent-clonal-complex-17-unveils-new-pathoadaptive-mutations
#16
Alexandre Almeida, Isabelle Rosinski-Chupin, Céline Plainvert, Pierre-Emmanuel Douarre, Maria J Borrego, Claire Poyart, Philippe Glaser
Group B Streptococcus (GBS) is a commensal of the gastrointestinal and genitourinary tracts, while a prevailing cause of neonatal disease worldwide. Of the various clonal complexes (CCs), CC17 is overrepresented in GBS-infected newborns for reasons that are still largely unknown. Here, we report a comprehensive genomic analysis of 626 CC17 isolates collected worldwide, identifying the genetic traits behind their successful adaptation to humans and the underlying differences between carriage and clinical strains...
September 2017: MSystems
https://www.readbyqxmd.com/read/28904997/development-of-inflammatory-bowel-disease-is-linked-to-a-longitudinal-restructuring-of-the-gut-metagenome-in-mice
#17
Thomas Sharpton, Svetlana Lyalina, Julie Luong, Joey Pham, Emily M Deal, Courtney Armour, Christopher Gaulke, Shomyseh Sanjabi, Katherine S Pollard
The gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late-stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regard to function. To investigate microbiome-mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where damped transforming growth factor β (TGF-β) signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis...
September 2017: MSystems
https://www.readbyqxmd.com/read/28861526/metabolic-network-analysis-and-metatranscriptomics-reveal-auxotrophies-and-nutrient-sources-of-the-cosmopolitan-freshwater-microbial-lineage-aci
#18
Joshua J Hamilton, Sarahi L Garcia, Brittany S Brown, Ben O Oyserman, Francisco Moya-Flores, Stefan Bertilsson, Rex R Malmstrom, Katrina T Forest, Katherine D McMahon
An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the "seed set framework," which computes the set of compounds that an organism must acquire from its environment (E...
July 2017: MSystems
https://www.readbyqxmd.com/read/28861525/impacts-of-penicillin-binding-protein-2-inactivation-on-%C3%AE-lactamase-expression-and-muropeptide-profile-in-stenotrophomonas-maltophilia
#19
Yi-Wei Huang, Yu Wang, Yun Lin, Chin Lin, Yi-Tsung Lin, Cheng-Chih Hsu, Tsuey-Ching Yang
Penicillin binding proteins (PBPs) are involved in peptidoglycan synthesis, and their inactivation is linked to β-lactamase expression in ampR-β-lactamase module-harboring Gram-negative bacteria. There are seven annotated PBP genes, namely, mrcA, mrcB, pbpC, mrdA, ftsI, dacB, and dacC, in the Stenotrophomonas maltophilia genome, and these genes encode PBP1a, PBP1b, PBP1c, PBP2, PBP3, PBP4, and PBP6, respectively. In addition, S. maltophilia harbors two β-lactamase genes, L1 and L2, whose expression is induced via β-lactam challenge...
July 2017: MSystems
https://www.readbyqxmd.com/read/28845461/large-scale-phylogenomics-of-the-lactobacillus-casei-group-highlights-taxonomic-inconsistencies-and-reveals-novel-clade-associated-features
#20
Sander Wuyts, Stijn Wittouck, Ilke De Boeck, Camille N Allonsius, Edoardo Pasolli, Nicola Segata, Sarah Lebeer
Although the genotypic and phenotypic properties of the Lactobacillus casei group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Here, we performed a large-scale comparative analysis by using 183 publicly available genomes supplemented with a Lactobacillus strain isolated from the human upper respiratory tract. On the basis of this analysis, we identified inconsistencies in the taxonomy and reclassified all of the genomes according to their most closely related type strains...
July 2017: MSystems
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