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https://www.readbyqxmd.com/read/28918349/inhibition-of-anaerobic-digestion-processes-applications-of-molecular-tools
#1
REVIEW
Yamrot M Amha, Muhammad Zohaib Anwar, Andrew Brower, Carsten S Jacobsen, Lauren B Stadler, Tara M Webster, Adam L Smith
Inhibition of anaerobic digestion (AD) due to perturbation caused by substrate composition and/or operating conditions can significantly reduce performance. Such perturbations could be limited by elucidating microbial community response to inhibitors and devising strategies to increase community resilience. To this end, advanced molecular methods are increasingly being applied to study the AD microbiome, a diverse community of microbial populations with complex interactions. This literature review of AD inhibition studies indicates that inhibitory concentrations are highly variable, likely stemming from differences in community structure or activity profile and previous exposure to inhibitors...
September 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28913777/diabetes-and-the-small-intestine
#2
REVIEW
Jonathan Gotfried, Stephen Priest, Ron Schey
Diabetes mellitus (DM) and its associated complications are becoming increasingly prevalent. Gastrointestinal symptoms associated with diabetes is known as diabetic enteropathy (DE) and may manifest as either diarrhea, fecal incontinence, constipation, dyspepsia, nausea, and vomiting or a combination of symptoms. The long-held belief that vagal autonomic neuropathy is the primary cause of DE has recently been challenged by newer theories of disease development. Specifically, hyperglycemia and the resulting oxidative stress on neural networks, including the nitrergic neurons and interstitial cells of Cajal (ICC), are now believed to play a central role in the development of DE...
September 15, 2017: Current Treatment Options in Gastroenterology
https://www.readbyqxmd.com/read/28903732/a-comparison-of-sequencing-platforms-and-bioinformatics-pipelines-for-compositional-analysis-of-the-gut-microbiome
#3
Imane Allali, Jason W Arnold, Jeffrey Roach, Maria Belen Cadenas, Natasha Butz, Hosni M Hassan, Matthew Koci, Anne Ballou, Mary Mendoza, Rizwana Ali, M Andrea Azcarate-Peril
BACKGROUND: Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines...
September 13, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28892653/saliva-derived-commensal-and-pathogenic-biofilms-in-a-human-gingiva-model
#4
J K Buskermolen, M M Janus, S Roffel, B P Krom, S Gibbs
In vitro models that closely mimic human host-microbiome interactions can be a powerful screening tool for antimicrobials and will hold great potential for drug validation and discovery. The aim of this study was to develop an organotypic oral mucosa model that could be exposed to in vitro cultured commensal and pathogenic biofilms in a standardized and scalable manner. The oral mucosa model consisted of a tissue-engineered human gingiva equivalent containing a multilayered differentiated gingiva epithelium (keratinocytes) grown on a collagen hydrogel, containing gingiva fibroblasts, which represented the lamina propria...
September 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28888103/using-crispr-cas-systems-as-antimicrobials
#5
REVIEW
David Bikard, Rodolphe Barrangou
Although CRISPR-Cas systems naturally evolved to provide adaptive immunity in bacteria and archaea, Cas nucleases can be co-opted to target chromosomal sequences rather than invasive genetic elements. Although genome editing is the primary outcome of self-targeting using CRISPR-based technologies in eukaryotes, self-targeting by CRISPR is typically lethal in bacteria. Here, we discuss how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death...
September 5, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28887527/pan-genome-analysis-of-bacillus-for-microbiome-profiling
#6
Yihwan Kim, InSong Koh, Mi Young Lim, Won-Hyong Chung, Mina Rho
Recent advances in high-throughput sequencing technology allow for in-depth studies on microbial genomes and their communities. While multiple strains of the same species could display genomic variations with different gene contents in diverse habitats and hosts, the essential functions for a specific species are conserved as core genes that are shared among strains. We have comprehensively analyzed 238 strains of five different Bacillus species to identify the properties of core and strain-specific genes. Core and strain-specific genes in each Bacillus species show significant differences in their functions and genomic signatures...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886168/unraveling-the-human-salivary-microbiome-diversity-in-indian-populations
#7
Anujit Sarkar, Mark Stoneking, Madhusudan R Nandineni
The importance of studying the salivary microbiome has been highlighted for its connection to health and disease and as a potential tool for supplementing human genetic diversity studies. While the salivary microbiome has been studied in various world populations, Indian populations have not been examined. We therefore analyzed microbiome diversity in saliva samples from 92 volunteers from eight different sampling locations in India by amplifying and sequencing variable regions (V1 and V2) of the bacterial 16S rRNA gene...
2017: PloS One
https://www.readbyqxmd.com/read/28885820/strategies-for-editing-virulent-staphylococcal-phages-using-crispr-cas10
#8
S M Nayeemul Bari, Forrest C Walker, Katie Cater, Barbaros Aslan, Asma Hatoum-Aslan
Staphylococci are prevalent skin-dwelling bacteria that are also leading causes of antibiotic-resistant infections. Viruses that infect and lyse these organisms (virulent staphylococcal phages) can be used as alternatives to conventional antibiotics and represent promising tools to eliminate or manipulate specific species in the microbiome. However, since over half their genes have unknown functions, virulent staphylococcal phages carry inherent risk to cause unknown downstream side effects. Further, their swift and destructive reproductive cycle make them intractable by current genetic engineering techniques...
September 8, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28872765/digital-therapy-in-diabetes
#9
REVIEW
Avivit Cahn, Amit Akirov, Itamar Raz
Diabetes care is largely dependent on patient self-management and empowerment, given that patients with diabetes must make numerous daily decisions of what to eat, when to exercise, and determine their insulin dose and timing if required. Additionally, patients and providers are generating vast amounts of data from many sources including electronic medical records, insulin pumps, sensors, glucometers, other wearables, as well as evolving genomic, proteomic, metabolomic and microbiomic data. Multiple digital tools and apps have been developed to assist patients to choose wisely, as well as enhance their compliance by employing motivational tools and incorporating incentives from social media and gaming techniques...
September 5, 2017: Journal of Diabetes
https://www.readbyqxmd.com/read/28872698/a-multivariate-distance-based-analytic-framework-for-microbial-interdependence-association-test-in-longitudinal-study
#10
Yilong Zhang, Sung Won Han, Laura M Cox, Huilin Li
Human microbiome is the collection of microbes living in and on the various parts of our body. The microbes living on our body in nature do not live alone. They act as integrated microbial community with massive competing and cooperating and contribute to our human health in a very important way. Most current analyses focus on examining microbial differences at a single time point, which do not adequately capture the dynamic nature of the microbiome data. With the advent of high-throughput sequencing and analytical tools, we are able to probe the interdependent relationship among microbial species through longitudinal study...
September 5, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28868052/high-resolution-microbiome-profiling-for-detection-and-tracking-of-salmonella-enterica
#11
Christopher J Grim, Ninalynn Daquigan, Tina S Lusk Pfefer, Andrea R Ottesen, James R White, Karen G Jarvis
16S rRNA community profiling continues to be a useful tool to study microbiome composition and dynamics, in part due to advances in next generation sequencing technology that translate into reductions in cost. Reliable taxonomic identification to the species-level, however, remains difficult, especially for short-read sequencing platforms, due to incomplete coverage of the 16S rRNA gene. This is especially true for Salmonella enterica, which is often found as a low abundant member of the microbial community, and is often found in combination with several other closely related enteric species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28867793/diet-gut-microbiome-and-epigenetics-emerging-links-with-inflammatory-bowel-diseases-and-prospects-for-management-and-prevention
#12
REVIEW
Krasimira Aleksandrova, Beatriz Romero-Mosquera, Vicent Hernandez
Inflammatory bowel diseases (IBD) represent a growing public health concern due to increasing incidence worldwide. The current notion on the pathogenesis of IBD is that genetically susceptible individuals develop intolerance to dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental triggers. Among the environmental factors associated with IBD, diet plays an important role in modulating the gut microbiome, influencing epigenetic changes, and, therefore, could be applied as a therapeutic tool to improve the disease course...
August 30, 2017: Nutrients
https://www.readbyqxmd.com/read/28859695/learning-microbial-community-structures-with-supervised-and-unsupervised-non-negative-matrix-factorization
#13
Yun Cai, Hong Gu, Toby Kenney
BACKGROUND: Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data...
August 31, 2017: Microbiome
https://www.readbyqxmd.com/read/28842539/dietary-fibers-and-protective-lactobacilli-drive-burrata-cheese-microbiome
#14
Fabio Minervini, Amalia Conte, Matteo Alessandro Del Nobile, Marco Gobbetti, Maria De Angelis
This study aimed at improving the functional attributes and shelf-life of burrata cheese by using protective lactobacilli (Lactobacillus plantarum LPAL and Lactobacillus rhamnosus LRB), fructoligosaccharides and inulin. Six burrata cheeses were made by using: i) the traditional protocol (control); ii) addition of 0.5% fructoligosaccharides and inulin (DF cheese); iii) protective lactobacilli in milk alone (PL cheese); iv) protective lactobacilli in milk and governing liquid (2PL cheese); v) protective lactobacilli in milk and dietary fibers (DF_PL cheese); and vi) protective lactobacilli in milk, governing liquid and dietary fibers (DF_2PL cheeses)...
August 25, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28834240/microbial-biotechnology-as-a-tool-to-restore-degraded-drylands
#15
Fernando T Maestre, Ricard Solé, Brajesh K Singh
We briefly review how microbial biotechnology can contribute to improve activities aiming to restore degraded drylands and to combat their desertification, which are an integral part of the Sustainable Development Goal 15 of the 2030 Agenda. Microbial biotechnology offers notable promise to improve restoration actions based on the use of biocrust-forming engineered cyanobacteria, which play key roles in maintaining ecosystem structure and functioning in drylands worldwide. Advances in our understanding of microbiome associated to biocrusts and of the signalling involved in the communication among their constituents can also potentially enhance the outcome of restoration activities in drylands...
August 22, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28831186/the-ibd-interactome-an-integrated-view-of-aetiology-pathogenesis-and-therapy
#16
REVIEW
Heitor S P de Souza, Claudio Fiocchi, Dimitrios Iliopoulos
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by chronic and heterogeneous manifestations, induced by interacting environmental, genomic, microbial and immunological factors. These interactions result in an overwhelming complexity that cannot be tackled by studying the totality of each pathological component (an '-ome') in isolation without consideration of the interaction among all relevant -omes that yield an overall 'network effect'. The outcome of this effect is the 'IBD interactome', defined as a disease network in which dysregulation of individual -omes causes intestinal inflammation mediated by dysfunctional molecular modules...
August 23, 2017: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28826742/a-comprehensive-review-and-update-on-crohn-s-disease
#17
Mahesh Gajendran, Priyadarshini Loganathan, Anthony P Catinella, Jana G Hashash
The term inflammatory bowel disease (IBD) refers principally to two major categories of chronic relapsing inflammatory intestinal disorders: Crohn's disease (CD) and ulcerative colitis (UC). In the United States, it is currently estimated that about 1.5 million people suffer from IBD, causing considerable suffering, mortality and economic loss every year. Yet the cause of IBD is unknown, and until we understand more, prevention or cure will not be possible. There is a lot of variation in the incidence and prevalence of CD based on geographic region, environment, immigrant population, and ethnic groups...
August 18, 2017: Disease-a-month: DM
https://www.readbyqxmd.com/read/28822770/regulation-of-autoimmune-myocarditis-by-host-responses-to-the-microbiome
#18
Jobert G Barin, Monica V Talor, Nicola L Diny, SuFey Ong, Julie A Schaub, Elizabeth Gebremariam, Djahida Bedja, Guobao Chen, Hee Sun Choi, Xuezhou Hou, Lei Wu, Ashley B Cardamone, Daniel A Peterson, Noel R Rose, Daniela Čiháková
The extensive, diverse communities that constitute the microbiome are increasingly appreciated as important regulators of human health and disease through inflammatory, immune, and metabolic pathways. We sought to elucidate pathways by which microbiota contribute to inflammatory, autoimmune cardiac disease. We employed an animal model of experimental autoimmune myocarditis (EAM), which results in inflammatory and autoimmune pathophysiology and subsequent maladaptive cardiac remodeling and heart failure. Antibiotic dysbiosis protected mice from EAM and fibrotic cardiac dysfunction...
August 16, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28793309/the-microbiome-in-urogenital-schistosomiasis-and-induced-bladder-pathologies
#19
Adewale S Adebayo, Mangesh Survayanshi, Shrikanth Bhute, Atinuke M Agunloye, Raphael D Isokpehi, Chiaka I Anumudu, Yogesh S Shouche
BACKGROUND: Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies...
August 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28766918/the-skin-microbiome-and-immune-system-potential-target-for-chemoprevention
#20
REVIEW
Mohammad Asif Sherwani, Saba Tufail, Anum Fatima Muzaffar, Nabiha Yusuf
There has been increasing interest in understanding the role of the human microbiome in skin diseases. Microbiome studies are being utilized in skin cancer research in numerous ways. Commensal bacteria are being studied as a potential tool to judge the biggest environmental risk of skin cancer, ultraviolet (UV) radiation. Owing to the recognized link of skin microbes in the process of inflammation, there have been theories linking commensal bacteria to skin cancer. Viral metagenomics has also provided insight into virus linked forms of skin cancers...
August 2, 2017: Photodermatology, Photoimmunology & Photomedicine
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