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Stool DNA

Francesco Multinu, Sean C Harrington, Jun Chen, Patricio R Jeraldo, Stephen Johnson, Nicholas Chia, Marina R Walther-Antonio
Variability in representation of microbial communities can be caused by differences in microbial composition or artifacts introduced at sample collection or processing. Alterations in community representation introduced by variations in starting DNA concentrations have not been systematically investigated in stool samples. The goal of this study was to evaluate the effect of the genomic DNA (gDNA) concentration in the resulting 16S rRNA gene library composition and compare its effect to other sample processing variables in homogenized human fecal material...
March 2018: MSphere
Hajri Al-Shehri, Artemis Koukounari, Michelle C Stanton, Moses Adriko, Moses Arinaitwe, Aaron Atuhaire, Narcis B Kabatereine, J Russell Stothard
Programmatic surveillance of intestinal schistosomiasis during control can typically use four diagnostic tests, either singularly or in combination, but these have yet to be cross-compared directly. Our study assembled a complete diagnostic dataset, inclusive of infection intensities, from 258 children from five Ugandan primary schools. The schools were purposely selected as typical of the endemic landscape near Lake Albert and reflective of high- and low-transmission settings. Overall prevalence was: 44.1% (95% CI 38...
March 21, 2018: Parasitology
Andrew K Fuller, Benjamin D Bice, Ashlee R Venancio, Olivia M Crowley, Ambur M Staab, Stephanie J Georges, Julio R Hidalgo, Annika V Warncke, Melinda L Angus-Hill
Several recent studies have illustrated the beneficial effects of living in an enriched environment on improving human disease. In mice, environmental enrichment (EE) reduces tumorigenesis by activating the mouse immune system, or affects tumor bearing animal survival by stimulating the wound repair response, including improved microbiome diversity, in the tumor microenvironment. Provided here is a detailed procedure to assess the effects of environmental enrichment on the biodiversity of the microbiome in a mouse colon tumor model...
February 28, 2018: Journal of Visualized Experiments: JoVE
Antonio Fadda, Davide Gentilini, Loredana Moi, Ludovic Barault, Vera Piera Leoni, Pia Sulas, Luigi Zorcolo, Angelo Restivo, Francesco Cabras, Federica Fortunato, Cesare Zavattari, Liliana Varesco, Viviana Gismondi, Maria Rosaria De Miglio, Antonio Mario Scanu, Federica Colombi, Pasquale Lombardi, Ivana Sarotto, Eleonora Loi, Francesco Leone, Silvia Giordano, Federica Di Nicolantonio, Amedeo Columbano, Patrizia Zavattari
Colorectal cancer (CRC) develops through the accumulation of both genetic and epigenetic alterations. However, while the former are already used as prognostic and predictive biomarkers, the latter are less well characterized. Here, performing global methylation analysis on both CRCs and adenomas by Illumina Infinium HumanMethylation450 Bead Chips, we identified a panel of 74 altered CpG islands, demonstrating that the earliest methylation alterations affect genes coding for proteins involved in the crosstalk between cell and surrounding environment...
March 15, 2018: International Journal of Cancer. Journal International du Cancer
Javier Gandasegui, Pedro Fernández-Soto, Antonio Muro, Constança Simões Barbosa, Fabio Lopes de Melo, Rodrigo Loyo, Elainne Christine de Souza Gomes
BACKGROUND: In Brazil, schistosomiasis is a parasitic disease of public health relevance, mainly in poor areas where Schistosoma mansoni is the only human species encountered and Biomphalaria straminea is one of the intermediate host snails. A nested-PCR based on a specific mitochondrial S. mansoni minisatellite DNA region has been successfully developed and applied as a reference method in Brazil for S. mansoni detection, mainly in host snails for epidemiological studies. The amplification efficiency of LAMP is known to be higher than PCR...
March 2018: PLoS Neglected Tropical Diseases
Gregory S Cooper, Sanford D Markowitz, Zhengyi Chen, Missy Tuck, Joseph E Willis, Barry M Berger, Dean E Brenner, Li Li
BACKGROUND: There is uncertainty as to the appropriate follow-up of patients who test positive on multimarker stool DNA (sDNA) testing and have a colonoscopy without neoplasia. AIMS: To determine the prevalence of missed colonic or occult upper gastrointestinal neoplasia in patients with an apparent false positive sDNA. METHODS: We prospectively identified 30 patients who tested positive with a commercially available sDNA followed by colonoscopy without neoplastic lesions...
March 7, 2018: Digestive Diseases and Sciences
Lisa F Stinson, Jeffrey A Keelan, Matthew S Payne
The establishment of human gut microbiota commences initially in utero . Meconium-the first fecal material passed after birth-can be used to study fetal gut contents; however, processing meconium samples for microbiome studies presents significant technical challenges. Meconium hosts a low biomass microbiome, is tar-like in texture and contains high concentrations of PCR inhibitors. This study aimed to evaluate four different DNA extraction methods to elucidate the most effective method for bacterial DNA recovery and sequencing analysis from first-pass meconium...
2018: Frontiers in Microbiology
Jasmohan S Bajaj, Leroy R Thacker, Andrew Fagan, Melanie B White, Edith A Gavis, Phillip B Hylemon, Robert Brown, Chathur Acharya, Douglas M Heuman, Michael Fuchs, Swati Dalmet, Masoumeh Sikaroodi, Patrick M Gillevet
BACKGROUND: Cirrhosis is associated with gut microbial changes, but current 16S rDNA techniques sequence both dead and live bacteria. We aimed to determine the rRNA content compared with DNA from the same stool sample to evaluate cirrhosis progression and predict hospitalizations. METHODS: Cirrhotics and controls provided stool for RNA and DNA analysis. Comparisons were made between cirrhotics/controls and within cirrhosis (compensated/decompensated, infected/uninfected, renal dysfunction/not, rifaximin use/not) with respect to DNA and RNA bacterial content using linear discriminant analysis...
March 8, 2018: JCI Insight
Feng Liao, Wenge Li, Wenpeng Gu, Wenzhu Zhang, Xiaoshu Liu, Xiaoqing Fu, Wen Xu, Yuan Wu, Jinxing Lu
To identify the prevalence and characteristics of community-acquired Clostridium difficile infection (CA-CDI) in southwest China, we conducted a cross-sectional study. 978 diarrhea patients were enrolled and stool specimens' DNA was screened for virulence genes. Bacterial culture was performed and isolates were characterized by PCR ribotyping and multilocus sequence typing. Toxin genes tcdA and/or tcdB were found in 138/978 (14.11%) cases for fecal samples. A total of 55 C. difficile strains were isolated (5...
March 5, 2018: Scientific Reports
Birson Ingti, Pranjit Saikia, Deepjyoti Paul, Anand Prakash Maurya, Debadatta Dhar Chanda, Atanu Chakravarty, Chandrayee Deshamukhya, Amitabha Bhattacharjee
OBJECTIVES: Plasmids of different replicon types are believed to be associated with the carriage and transmission of antibiotic resistance genes. Thus present study was undertaken to check the association of CIT with particular plasmid types and to identify the E. coli strains involve in the maintenance of this determinant within the plasmid. METHODS: Screening of AmpC β-lactamase phenotypically by Modified Three Dimensional Extract Method followed by Antimicrobial Susceptibility and MIC determination...
March 2, 2018: Journal of Global Antimicrobial Resistance
Mengistu Damitie, Zeleke Mekonnen, Tadesse Getahun, Dante Santiago, Luc Leyns
BACKGROUND: Giardia duodenalis is a species complex consisting of multiple genetically distinct assemblages. The species imposes a major public health crisis on developing countries. However, the molecular diversity, transmission dynamics and risk factors of the species in these countries are indeterminate. This study was conducted to determine the molecular epidemiology of G. duodenalis infection in asymptomatic individuals in Southern Ethiopia. METHODS: From March to June 2014, fresh stool samples were collected from 590 randomly selected individuals...
March 5, 2018: Infectious Diseases of Poverty
Maria Cristina Angelici, Chiara Nardis, Riccardo Scarpelli, Paola Ade
In the reported case, a 41-year-old Italian man came to the clinician's observation reporting cramps, bloating and watery diarrhoea a few days after drinking water indicated as unpotable from a fountain in a farm area. The medical suspicion was directed at both gluten intolerance and enteric infection, eventually of waterborne origin. Gluten intolerance was investigated by intestinal biopsy and excluded, while stool analyses ruled out infective bacteriological or viral agents and parasites. Subsequently, a persistent eosinophilia was revealed and a parasitological analysis was again suggested, planning for a more sensitive molecular method...
March 2, 2018: New Microbiologica
Elham Kord-Sarkachi, Mehdi Tavalla, Moluok Beiromvand
Microsporidia is often considered as an opportunistic infection in patients with impaired immune systems such as patients with acquired immune deficiency syndrome, transplant recipients, children and old people. Due to the ability of the parasite to transmit from animals to human as well as the increasing prevalence of parasitic infections and immune deficiency diseases; therefore, the aim of this study was to evaluate molecular diagnosis of microsporidia strains in slaughtered cows of southwest of Iran. Initially, 256 stool samples of cows were collected from 5 regions of Khuzestan province, southwest of Iran and stained by modified trichrome (weber)...
March 2018: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
Anahita Razavi Piranshahi, Mehdi Tavalla, Shahram Khademvatan
Blastocystis hominis ( B. hominis ) is a protozoan zoonosis which clinical signs of infection with this parasite has been reported to be more severe in patients with weakened immune systems than healthy controls. So, the aim of the study was to evaluate genomic analysis of B. hominis isolates obtained from patients with HIV-positive using locus SSU-rDNA. At first, 268 stool samples were randomly collected from patients with HIV-positive referred to health centers of Khuzestan province, southwest of Iran. Formol-ether and direct smear techniques were used for the detection of parasitic agents...
March 2018: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
Wei-Kai Wu, Chieh-Chang Chen, Suraphan Panyod, Rou-An Chen, Ming-Shiang Wu, Lee-Yan Sheen, Shan-Chwen Chang
Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP)...
February 25, 2018: Journal of the Formosan Medical Association, Taiwan Yi Zhi
Jung-Ho Park, Jae-Woo Lee, Hoonsung Choi, Sun Keun Jung, Jeom Sun Kim, Kyung-Woon Kim, Keon Bong Oh, Hyeon Yang, Sung June Byun
Previously, Escherichia coli harboring the codon-optimized 3D8scFv gene (E. coli 3D8scFv) was developed as a feed additive for use in preventing norovirus infection. Here, we evaluated whether the 3D8scFv gene affects the colonization of E coli when E. coli 3D8scFv passes through the mouse gastrointestinal tract. To determine the colonization ability of E. coli 3D8scFv, E. coli cells with or without the 3D8scFv gene were fed to mice. Total DNA was extracted from the animals' stools, stomach, small intestine and colon...
February 24, 2018: Regulatory Toxicology and Pharmacology: RTP
S M B Duarte, J T Stefano, L Miele, F R Ponziani, M Souza-Basqueira, L S R R Okada, F G de Barros Costa, K Toda, D F C Mazo, E C Sabino, F J Carrilho, A Gasbarrini, C P Oliveira
BACKGROUND AND AIM: The aim of the study was to compare the gut microbiomes from obese and lean patients with or without NASH to outline phenotypic differences. METHODS AND RESULTS: We performed a cross-sectional pilot study comprising biopsy-proven NASH patients grouped according to BMI. Microbiome DNA was extracted from stool samples, and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion PGM Torrent platform, and data were analyzed using QIIME software...
October 26, 2017: Nutrition, Metabolism, and Cardiovascular Diseases: NMCD
Shaghayegh Baradaran Ghavami, Elham Rostami, Abbas Akhavan Sephay, Shabnam Shahrokh, Hedieh Balaii, Hamid Asadzadeh Aghdaei, Mohammad Reza Zali
It is hypothesized that direct and indirect homeostasis between gut microbiota plays a key role in different intestine disorders. Archaea methanogens, an ancient domain of single-celled organism, are major archaea in the digestive system. Recent evidence has shown that the variable prevalence of methanogens in different individuals could have certain effects on inflammatory bowel diseases (IBD). We aimed to assess the prevalence of Methanobrevibacter smithii between Iranian patients suffering from IBD and healthy control subjects...
February 22, 2018: Microbial Pathogenesis
Dorothy E Loy, Meagan A Rubel, Alexa N Avitto, Weimin Liu, Yingying Li, Gerald H Learn, Alessia Ranciaro, Eric Mbunwe, Charles Fokunang, Alfred K Njamnshi, Paul M Sharp, Sarah A Tishkoff, Beatrice H Hahn
African apes are endemically infected with numerous Plasmodium spp. including close relatives of human Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, and Plasmodium malariae. Although these ape parasites are not believed to pose a zoonotic threat, their ability to colonise humans has not been fully explored. In particular, it remains unknown whether ape parasites are able to initiate exo-erythrocytic replication in human hepatocytes following the bite of an infective mosquito. Since animal studies have shown that liver stage infection can result in the excretion of parasite nucleic acids into the bile, we screened faecal samples from 504 rural Cameroonians for Plasmodium DNA...
February 21, 2018: International Journal for Parasitology
Liu Xiao-Jie, Mao Tie-Bo, Wu Peng, Zhou Rui
OBJECTIVE: To understand the prevalence of Cryptosporidium infection in diarrhea infants under 2 years old in Wuhan City, so as to provide the epidemiological evidence for the prevention and treatment of cryptosporidiosis. METHODS: The fecal samples from infants under 2 years old with diarrhea were collected in Hubei General Hospital and Central South Hospital in Wuhan City, Hubei Province from August 2014 to July 2015. The fecal samples were stored in 2.5% potassium dichromate at 4 ℃ after filtered...
March 14, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
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