keyword
https://read.qxmd.com/read/38474213/improved-dna-extraction-and-amplification-strategy-for-16s-rrna-gene-amplicon-based-microbiome-studies
#1
JOURNAL ARTICLE
Bo-Young Hong, Mark Driscoll, Dawn Gratalo, Thomas Jarvie, George M Weinstock
Next-generation sequencing technology has driven the rapid advancement of human microbiome studies by enabling community-level sequence profiling of microbiomes. Although all microbiome sequencing methods depend on recovering the DNA from a sample as a first critical step, lysis methods can be a major determinant of microbiome profile bias. Gentle enzyme-based DNA preparation methods preserve DNA quality but can bias the results by failing to open difficult-to-lyse bacteria. Mechanical methods like bead beating can also bias DNA recovery because the mechanical energy required to break tougher cell walls may shear the DNA of the more easily lysed microbes, and shearing can vary depending on the time and intensity of beating, influencing reproducibility...
March 4, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38461289/gut-microbial-network-signatures-of-early-colonizers-in-preterm-neonates-with-extrauterine-growth-restriction
#2
JOURNAL ARTICLE
Yumei Liang, Xiaomin Yao, Zida Meng, Jinyun Lan, Yanqing Qiu, Chao Cen, Yanni Feng
BACKGROUND: Extrauterine growth restriction (EUGR) represents a prevalent condition observed in preterm neonates, which poses potential adverse implications for both neonatal development and long-term health outcomes. The manifestation of EUGR has been intricately associated with perturbations in microbial and metabolic profiles. This study aimed to investigate the characteristics of the gut microbial network in early colonizers among preterm neonates with EUGR. METHODS: Twenty-nine preterm infants participated in this study, comprising 14 subjects in the EUGR group and 15 in the normal growth (AGA) group...
March 9, 2024: BMC Microbiology
https://read.qxmd.com/read/38459466/genome-mining-of-escherichia-coli-wg5d-from-drinking-water-source-unraveling-antibiotic-resistance-genes-virulence-factors-and-pathogenicity
#3
JOURNAL ARTICLE
Oluwaseyi Samuel Olanrewaju, Lesego G Molale-Tom, Rinaldo K Kritzinger, Cornelius Carlos Bezuidenhout
BACKGROUND: Escherichia coli, a ubiquitous inhabitant of the gut microbiota, has been recognized as an indicator of fecal contamination and a potential reservoir for antibiotic resistance genes. Its prevalence in drinking water sources raises concerns about the potential dissemination of antibiotic resistance within aquatic ecosystems and the subsequent impact on public health. The ability of E. coli to acquire and transfer resistance genes, coupled with the constant exposure to low levels of antibiotics in the environment, underscores the need for comprehensive surveillance and rigorous antimicrobial stewardship strategies to safeguard the quality and safety of drinking water supplies, ultimately mitigating the escalation of antibiotic resistance and its implications for human well-being...
March 8, 2024: BMC Genomics
https://read.qxmd.com/read/38457002/first-report-of-giardia-duodenalis-in-dairy-cattle-and-beef-cattle-in-shanxi-china
#4
JOURNAL ARTICLE
Li Zhao, Yan Wang, Mingyuan Wang, Shan Zhang, Lifeng Wang, Zhansheng Zhang, Hailiang Chai, Chao Yi, Wenjun Fan, Yonghong Liu
BACKGROUND: Giardia duodenalis is an important intestinal parasitic protozoan that infects several vertebrates, including humans. Cattle are considered the major source of giardiasis outbreak in humans. This study aimed to investigate the prevalence and multilocus genotype (MLG) of G. duodenalis in Shanxi, and lay the foundation for the prevention and control of Giardiosis. METHODS AND RESULTS: DNA extraction, nested polymerase chain reaction, sequence analysis, MLG analysis, and statistical analysis were performed using 858 bovine fecal samples from Shanxi based on three gene loci: β-giardin (bg), glutamate dehydrogenase (gdh), and triosephosphate isomerase (tpi)...
March 8, 2024: Molecular Biology Reports
https://read.qxmd.com/read/38451230/a-comparison-of-short-read-hifi-long-read-and-hybrid-strategies-for-genome-resolved-metagenomics
#5
JOURNAL ARTICLE
Raphael Eisenhofer, Joseph Nesme, Luisa Santos-Bay, Adam Koziol, Søren Johannes Sørensen, Antton Alberdi, Ostaizka Aizpurua
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data...
March 7, 2024: Microbiology Spectrum
https://read.qxmd.com/read/38450718/molecular-prevalence-and-subtype-distribution-of-blastocystis-spp-among-children-who-have-diarrheia-or-are-asymptomatic-in-wenzhou-zhejiang-province-china
#6
JOURNAL ARTICLE
Wei Zhao, Guangxu Ren, Long Wang, Lisha Xie, Jiayang Wang, Jialiang Mao, Yanbin Sun, Gang Lu, Huicong Huang
Blastocystis sp., a significant zoonotic parasite with a global distribution, was the focus of this study, which aimed to investigate its prevalence and genetic diversity among diarrheic and asymptomatic children in Wenzhou, China. We collected 1,032 fecal samples from Yuying Children's Hospital, Wenzhou, China, comprising 684 from children with diarrhea and 348 from asymptomatic children. Genomic DNA extracted from these samples was used to detect Blastocystis spp. by PCR, targeting the small subunit ribosomal RNA gene...
2024: Parasite: Journal de la Société Française de Parasitologie
https://read.qxmd.com/read/38430046/diagnostic-advancements-isolating-mycobacterium-avium-ssp-paratuberculosis-and-unveiling-its-molecular-identity-with-nested-pcr
#7
JOURNAL ARTICLE
Faranak Nouri, Alireza Shahrjerdi, Hossein Ali Zarnegarpour, Nader Mosvari
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of paratuberculosis, which is currently prevalent in many parts of Iran and produces severe economic loss. It is hence necessary to identify and isolate the animals infected with this bacterium, so this research aimed to isolate MAP from milk and fecal samples of ELISA-positive animals and determine the molecular identity of isolates. After performing ELISA on 3,700 bovine blood samples, 115 samples of milk and feces were taken from ELISA-positive cattle and were cultured on Herald's egg yolk medium with and without mycobactin-J and then the acid-fastness of positive samples was determined using Ziehl-Neelsen staining...
February 29, 2024: Cellular and Molecular Biology
https://read.qxmd.com/read/38393127/molecular-prevalence-and-subtypes-distribution-of-blastocystis-spp-in-humans-of-latin-america-a-systematic-review
#8
REVIEW
Carmine Fusaro, Jaime E Bernal, Rosa Baldiris-Ávila, Rafael González-Cuello, Julio Cisneros-Lorduy, Arley Reales-Ruiz, Raimundo Castro-Orozco, Yohanna Sarria-Guzmán
Blastocystis spp. are among the few enteric parasites with a prevalence that can reach up to approximately 80% in communities of developing countries. This systematic review updates and summarizes available literature on the molecular prevalence and subtype distribution of Blastocystis spp. in Latin American people. This work follows the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. The literature revised covers from 1 January 2015 to 6 October 2023 in seven different scientific databases, and the material was selected through inclusion and exclusion criteria...
February 1, 2024: Tropical Medicine and Infectious Disease
https://read.qxmd.com/read/38388738/emergence-of-a-clinical-salmonella-enterica-serovar-1-4-5-12-i-isolate-st3606-in-china-with-susceptibility-decrease-to-ceftazidime-avibactam-carrying-a-novel-bla-ctx-m-261-variant-and-a-bla-ndm-5
#9
JOURNAL ARTICLE
Jie Wei, Shimei Shen, Qinghuan Zhang, Jinping Lu, Shenglan Mao, Chunhong Zou, Hua Zhou, YeLin Wei, Xingyi Ou, Jinyu Huang, Deqiang Wang, Xiaobin Li, Qun Wan, Baoju Shan, Zhenlin Zhang
PURPOSE: The detection rate of Salmonella enterica serovar 1,4,[5], 12: i: - (S. 1,4,[5], 12: i: -) has increased as the most common serotype globally. A S. 1,4,[5], 12: i: - strain named ST3606 (sequence type 34), isolated from a fecal specimen of a child with acute diarrhea hospitalized in a tertiary hospital in China, was firstly reported to be resistant to carbapenem and ceftazidime-avibactam. The aim of this study was to characterize the whole-genome sequence of S. 1,4,[5], 12: i: - isolate, ST3606, and explore its antibiotic resistance genes and their genetic environments...
February 22, 2024: European Journal of Clinical Microbiology & Infectious Diseases
https://read.qxmd.com/read/38366085/choice-of-dna-extraction-method-affects-stool-microbiome-recovery-and-subsequent-phenotypic-association-analyses
#10
JOURNAL ARTICLE
Asier Fernández-Pato, Trishla Sinha, Ranko Gacesa, Sergio Andreu-Sánchez, Milla F Brandao Gois, Jody Gelderloos-Arends, Dianne B H Jansen, Marloes Kruk, Martin Jaeger, Leo A B Joosten, Mihai G Netea, Rinse K Weersma, Cisca Wijmenga, Hermie J M Harmsen, Jingyuan Fu, Alexandra Zhernakova, Alexander Kurilshikov
The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity...
February 16, 2024: Scientific Reports
https://read.qxmd.com/read/38332014/temporal-variations-in-the-gut-microbial-diversity-in-response-to-high-fat-diet-and-exercise
#11
JOURNAL ARTICLE
Saba Imdad, Byunghun So, Junho Jang, Jinhan Park, Sam-Jun Lee, Jin-Hee Kim, Chounghun Kang
High-fat diet-induced obesity is a pandemic caused by an inactive lifestyle and increased consumption of Western diets and is a major risk factor for diabetes and cardiovascular diseases. In contrast, exercise can positively influence gut microbial diversity and is linked to a decreased inflammatory state. To understand the gut microbial variations associated with exercise and high-fat diet over time, we conducted a longitudinal study to examine the effect of covariates on gut microbial diversity and composition...
February 8, 2024: Scientific Reports
https://read.qxmd.com/read/38329115/prescription-opioids-induced-microbial-dysbiosis-worsens-severity-of-chronic-pancreatitis-and-drives-pain-hypersensitivity
#12
JOURNAL ARTICLE
Kousik Kesh, Junyi Tao, Nillu Ghosh, Richa Jalodia, Salma Singh, Rajinder Dawra, Sabita Roy
Opioids, such as morphine and oxycodone, are widely used for pain management associated with chronic pancreatitis (CP); however, their impact on the progression and pain sensitivity of CP has never been evaluated. This report investigates the impact of opioid use on the severity of CP, pain sensitivity, and the gut microbiome. C57BL/6 mice were divided into control, CP, CP with morphine/oxycodone, and either morphine or oxycodone alone groups. CP was induced by administration of caerulein (50ug/kg/h, i.p. hourly x7, twice a week for 10 weeks)...
2024: Gut Microbes
https://read.qxmd.com/read/38324560/fecal-microbiome-composition-and-diversity-of-cryopreserved-canine-stool-at-different-duration-and-storage-conditions
#13
JOURNAL ARTICLE
Patrick Barko, Julie Nguyen-Edquilang, David A Williams, Arnon Gal
Fresh-frozen stool banks intended for humans with gastrointestinal and metabolic disorders have been recently established and there are ongoing efforts to establish the first veterinary fresh-frozen stool bank. Fresh frozen stored feces provide an advantage of increased availability and accessibility to high-quality optimal donor fecal material. The stability of frozen canine feces regarding fecal microbiome composition and diversity has not been reported in dogs, providing the basis for this study. We hypothesized that fecal microbial composition and diversity of healthy dogs would remain stable when stored at -20°C and -80°C for up to 12 months compared to baseline samples evaluated before freezing...
2024: PloS One
https://read.qxmd.com/read/38316862/acute-gastrointestinal-permeability-after-traumatic-brain-injury-in-mice-precedes-a-bloom-in-akkermansia-muciniphila-supported-by-intestinal-hypoxia
#14
JOURNAL ARTICLE
Anthony J DeSana, Steven Estus, Terrence A Barrett, Kathryn E Saatman
Traumatic brain injury (TBI) increases gastrointestinal morbidity and associated mortality. Clinical and preclinical studies implicate gut dysbiosis as a consequence of TBI and an amplifier of brain damage. However, little is known about the association of gut dysbiosis with structural and functional changes of the gastrointestinal tract after an isolated TBI. To assess gastrointestinal dysfunction, mice received a controlled cortical impact or sham brain injury and intestinal permeability was assessed at 4 h, 8 h, 1 d, and 3 d after injury by oral administration of 4 kDa FITC Dextran prior to euthanasia...
February 5, 2024: Scientific Reports
https://read.qxmd.com/read/38316105/the-fecal-bacterial-microbiota-is-not-useful-for-discriminating-between-lymphoplasmacytic-enteritis-and-low-grade-intestinal-t-cell-lymphoma-in-cats-nor-for-predicting-therapeutic-response
#15
JOURNAL ARTICLE
Elena Benvenuti, Riccardo Ferriani, Paola Gianella, Pietro Ruggiero, Federica Cagnasso, Antonio Borrelli, Giuseppe Benvenuto, Loris Bertoldi, Enrico Bottero
OBJECTIVE: To evaluate the fecal bacterial microbiota at the time of diagnosis (T0) and after 1 month of therapy (T1) in cats diagnosed with lymphoplasmacytic enteritis (LPE) or cats with low-grade intestinal T-cell lymphoma (LGITL) and to compare these findings with those of healthy cats. ANIMALS: 5 healthy cats, 13 cats with LPE, and 7 cats with LGITL were prospectively enrolled between June 2020 and June 2021. METHODS: Fecal samples were collected at T0 and T1, and DNA was extracted for 16S ribosomal amplicon sequencing...
February 9, 2024: American Journal of Veterinary Research
https://read.qxmd.com/read/38302245/assessing-microbiota-composition-in-the-context-of-aging
#16
JOURNAL ARTICLE
Diana Campos-Iglesias, José M P Freije, Carlos López-Otín
The gut microbiota is a complex community of different microbial species that influence many aspects of health. Consequently, shifts in the composition of gut microbiome have been proposed to exert negative effects on the host physiology, leading to the pathogenesis of various age-related disorders, including cardiovascular and neurological diseases, type 2 diabetes, obesity, non-alcoholic liver disease, and other pathological conditions. Thus, understanding how the gut microbiota influences the aging-related decline is particularly topical...
2024: Methods in Cell Biology
https://read.qxmd.com/read/38297429/dna-metabarcoding-diet-analysis-in-a-generalist-omnivore-feeding-trials-reveal-the-efficacy-of-extraction-kits-and-a-multi-locus-approach-for-identifying-diverse-diets
#17
JOURNAL ARTICLE
Kantima Thongjued, Karina Garcia, Delia Scott, David J Gonthier, Julian R Dupuis
Metabarcoding-based diet analysis is a valuable tool for understanding the feeding behavior of a wide range of species. However, many studies using these methods for wild animals assume accuracy and precision without experimental evaluation with known positive control food items. Here, we conducted a feeding trial experiment with a positive control community in pasture-raised chickens and assessed the efficacy of several commonly used DNA extraction kits and primer sets. We hand-fed 22 known food items, including insects and plants, to six backyard laying hens and collected their excreta for eight h...
January 31, 2024: Integrative Zoology
https://read.qxmd.com/read/38294580/fecal-microbiota-transplantation-alleviates-allergic-rhinitis-via-cd4-t-cell-modulation-through-gut-microbiota-restoration
#18
JOURNAL ARTICLE
Lin Dong, Yulei Tang, Silu Wen, Yan He, Fen Li, Yuqin Deng, Zezhang Tao
Allergic rhinitis (AR) is an allergic condition of the upper respiratory tract with a complex pathogenesis, including epithelial barrier disruption, immune regulation, and gut microbiota, which is not yet fully understood. Gut microbiota is closely linked to allergic diseases, including AR. Fecal microbiota transplantation (FMT) has recently been recognized as a potentially effective therapy for allergic diseases. However, the efficacy and mechanism of action of FMT in AR remain unknown. Herein, we aimed to observe the implications of gut microbiota on epithelial barrier function and T cell homeostasis, as well as the effect of FMT in AR, using the ovalbumin (OVA)-induced AR mice...
January 31, 2024: Inflammation
https://read.qxmd.com/read/38285680/impact-of-fecal-sample-preservation-and-handling-techniques-on-the-canine-fecal-microbiota-profile
#19
JOURNAL ARTICLE
Olivia Chiu, Diego E Gomez, Dasiel Obrego, Kari Dunfield, Jennifer L MacNicol, Brooklynn Liversidge, Adronie Verbrugghe
Canine fecal microbiota profiling provides insight into host health and disease. Standardization of methods for fecal sample storage for microbiomics is currently inconclusive, however. This study investigated the effects of homogenization, the preservative RNAlater, room temperature exposure duration, and short-term storage in the fridge prior to freezing on the canine fecal microbiota profile. Within 15 minutes after voiding, samples were left non-homogenized or homogenized and aliquoted, then kept at room temperature (20-22°C) for 0...
2024: PloS One
https://read.qxmd.com/read/38281761/improved-molecular-identification-of-strongyloides-myopotami-in-nutrias-using-fecalsamples
#20
JOURNAL ARTICLE
Yuga Mori, Atsushi Naka, Ryosuke Koda, Yuzuru Ishizuka, Atsushi Hinenoya, Tomoyuki Shibahara, Kazumi Sasai, Makoto Matsubayashi
Strongyloides myopotami is an intestinal nematode parasite of nutrias. Identification of S. myopotami is conducted based on the morphological characteristics of adult worms or cultured larvae. To widely and effectively understand the infection in nutrias, it would be preferable to develop the molecular identification using a few grams of the feces. Here, we attempted to identify S. myopotami using DNA extracted from eggs obtained from fecal samples. Among previously reported primer pairs targeting the 18S rRNA gene of Strongyloides spp...
January 26, 2024: Journal of Veterinary Medical Science
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