Article
Agriculture, Dairy & Animal Science
Mariya Gryaznova, Yuliya Smirnova, Inna Burakova, Polina Morozova, Ekaterina Nesterova, Mariya Gladkikh, Evgeny Mikhaylov, Mikhail Syromyatnikov
Summary: This study aimed to investigate the composition of the microbiome in newborn piglets with diarrhea to identify relevant markers of the disease. The results showed no bacterial and eukaryotic aberrations in the fecal microbiome of diarrheal piglets but higher levels of bacterial diversity, which may be associated with dysbacteriosis and inflammation. Additionally, an increase in the abundance of Bacteroides B40-8 phage was observed in the observation group, while an increase in the abundance of Escherichia virus BP4 was found in the healthy group.
Article
Gastroenterology & Hepatology
Anthony Mannion, Alexander Sheh, Zeli Shen, JoAnn Dzink-Fox, M. Blanca Piazuelo, Keith T. Wilson, Richard Peek, James G. G. Fox
Summary: In this study, whole metagenomic shotgun sequencing (WMS) was used to survey the microbiome in gastric biopsy samples from high-risk and low-risk gastric cancer towns in Colombia. WMS demonstrated its capability to identify and characterize bacterial taxa and functional profiles of the gastric microbiome, with advantages over traditional culture and 16S rRNA sequencing. WMS detected more bacterial taxa and risk factors for H. pylori-associated gastric disease compared to other sequencing approaches.
Article
Immunology
Miranda Stiernborg, J. W. Debelius, Liu L. Yang, Elin Skott, Vincent Millischer, MaiBritt Giacobini, Philippe A. Melas, Fredrik Boulund, Catharina Lavebratt
Summary: Recent evidence suggests that there is a link between neurodevelopmental disorders, such as ADHD, and the gut microbiome. A study was conducted with 147 well-characterized adult and child ADHD patients to investigate the impact of psychostimulant medication on the gut microbiome. The findings showed significant differences in bacterial strains, bacterial genes, inflammatory markers, and short-chain fatty acids between ADHD patients and controls, as well as between medicated and non-medicated children with ADHD.
BRAIN BEHAVIOR AND IMMUNITY
(2023)
Article
Microbiology
Yanping Xu, Olivia Milburn, Traci Beiersdorfer, Lizhong Du, Henry Akinbi, David B. Haslam
Summary: This study found that early brief exposure to antibiotics significantly disrupts the developmental trajectory of the neonatal microbiome, leading to a corresponding impairment in its metabolic functional capacity. Infants not exposed to antibiotics had higher abundance of butyrate-producing genera and increased metabolic pathways for short-chain fatty acid synthesis at 3 weeks postnatally.
Article
Microbiology
Diksha Klair, Shefali Dobhal, Amjad Ahmad, Zohaib Ul Hassan, Jensen Uyeda, Joshua Silva, Koon-Hui Wang, Seil Kim, Anne M. Alvarez, Mohammad Arif
Summary: Irrigation water serves as a common source of contamination in agriculture, carrying plant and foodborne human pathogens and providing a habitat for microbial proliferation. This study investigated the bacterial communities and their functions in irrigation water from wetland taro farms in Hawaii, using different DNA sequencing platforms. The results showed that Illumina reads provided comprehensive taxonomic classification, with Proteobacteria being the most abundant phylum in stream source and associated water samples. Cyanobacteria dominated tank and spring water samples, while Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, a significant portion of the short amplicon reads remained unclassified at the species level. In contrast, Oxford Nanopore MinION was better for microbe classification at the genus and species levels, while shotgun metagenome data did not yield reliable taxonomic classification results. Functional analysis revealed a limited overlap of genes between consortia and the presence of antibiotic resistance genes. Comprehensive understanding of microbial communities and their functions is crucial for developing effective water management strategies to ensure safe fresh produce and protect health and environment. Quantitative comparisons highlighted the importance of selecting appropriate analytical methods based on the desired level of taxonomic delineation in each microbiome.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Zixuan Xie, Aleix Canalda-Baltrons, Christophe d'Enfert, Chaysavanh Manichanh
Summary: The study demonstrates that shotgun DNA sequencing combined with a new enrichment protocol and a comprehensive fungal database provides a cost-effective approach to analyze the gut mycobiome at the species level and integrate bacterial and fungal community analyses in fecal samples. The mycobiome is more variable than the bacterial community in terms of composition and functions. Microbial diversity, composition, and functions are associated with habitual diet composition rather than global dietary changes.
Article
Microbiology
Sankhya Bommana, Gracie Richards, Mike Kama, Reshma Kodimerla, Kenan Jijakli, Timothy D. Read, Deborah Dean
Summary: Chlamydia trachomatis is the primary cause of bacterial sexually transmitted infections worldwide. This study investigates the microbial composition and function in the vagina, endocervix, and rectum of Fijian women with and without C. trachomatis infections. The results show unique microbial profiles in C. trachomatis-infected women, with more complex microbial pathways in the endocervix compared to the vagina. In addition, some women showed similarities in microbiome composition across different sites, suggesting potential intragenitorectal transmission. This study highlights the importance of understanding genitorectal microbiomes in promoting C. trachomatis infection and calls for larger prospective studies to better define the microbiomes of Pacific Islanders.
MICROBIOLOGY SPECTRUM
(2022)
Review
Gastroenterology & Hepatology
Yinglin Xia
Summary: Mounting evidence has shown a link between gut microbiome and various cancers, but analyzing microbiome data poses challenges and requires proper statistical methods and normalization. This review provides an overview of the unique characteristics of microbiome data and the available normalization methods in microbiome cancer research using examples. The evaluation of these normalization methods is also comprehensively investigated.
Article
Microbiology
Zhicheng Ji, Li Ma
Summary: In analyzing metatranscriptomics data, it is important to control for both DNA and taxa abundances to eliminate their strong correlation with RNA abundance.
Article
Microbiology
Matthew Y. Cho, Marc Oliva, Anna Spreafico, Bo Chen, Xu Wei, Yoojin Choi, Rupert Kaul, Lillian L. Siu, Bryan Coburn, Pierre H. H. Schneeberger
Summary: In this study, a quantitative PCR-based assay was used to predict host-to-microbe ratios before sequencing, validated on two sample types, and showed accurate prediction across a range of sample compositions. This easy-to-use assay can help researchers plan their shotgun sequencing experiments more efficiently by predicting human-to-microbe ratios.
Article
Microbiology
Shyam Sundar Paul, Savaram Venkata Rama Rao, Nagendra Hegde, Nicola J. Williams, Rudra Nath Chatterjee, Mantena Venkata Lakshmi Narasimha Raju, Godumagadda Narender Reddy, Vikas Kumar, Prakki Santosh Phani Kumar, Sathi Mallick, Madhuranjana Gargi
Summary: Studies have shown that the use of antimicrobial growth promoters (AGPs) in broiler production does not significantly affect productivity and feed efficiency, but it can affect the selection of antibiotic resistance genes (ARGs). AGPs do not have a significant impact on gut bacterial community structure, but can reduce the population density of certain potential pathogenic bacteria. Therefore, there is a need to reduce the use of AGPs and monitor the spread of ARGs in broiler chicken production.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Psychology, Clinical
Wen-tao Lai, Wen-feng Deng, Shu-xian Xu, Jie Zhao, Dan Xu, Yang-hui Liu, Yuan-yuan Guo, Ming-bang Wang, Fu-sheng He, Shu-wei Ye, Qi-fan Yang, Tie-bang Liu, Ying-li Zhang, Sheng Wang, Min-zhi Li, Ying-jia Yang, Xin-hui Xie, Han Rong
Summary: This study found changes in gut microbiota and the Trp pathway in MDD patients, with an increase in Bifidobacterium levels and decreased abundances of certain KEGG orthologies in the MiTBamp. A negative correlation was also observed between K01626 abundance and HAMD scores in the MDD group. The findings suggest that alterations in gut microbiota could potentially serve as biomarkers for distinguishing MDD patients from healthy controls.
PSYCHOLOGICAL MEDICINE
(2021)
Article
Engineering, Environmental
Yang Song, Rachel Finkelstein, William Rhoads, Marc A. Edwards, Amy Pruden
Summary: This study investigates the effects of copper on the microbial community in hot water plumbing systems. The results show that even low doses of copper can have an impact on the broader microbial community and that opportunistic pathogens in the system are highly copper tolerant. The addition of orthophosphate can reduce the bioavailability of copper. Functional gene analysis suggests that membrane damage and interruption of nucleic acid replication may be involved in the copper inactivation mechanisms.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Environmental Sciences
Vignesh Kumar Balasubramanian, Midhuna Immaculate Joseph Maran, Darwin Ramteke, Deepak Samuel Vijaykumar, Abhilash Kottarathail Rajendran, Purvaja Ramachandran, Ramesh Ramachandran
Summary: A metagenomics study on environmental DNA collected from an urban backwater area in southeast India revealed the potential of identifying small micro-eukaryote species and highlighted the presence of organisms of conservational significance and ecological importance in the ecosystem. This approach also showed the existence of pathogenic microorganisms due to sewage mixing with the backwaters, recommending it for an initial assessment of biodiversity structure in an ecosystem for biomonitoring programs.
MARINE POLLUTION BULLETIN
(2021)
Article
Oncology
Yaohua Yang, Jirong Long, Cong Wang, William J. Blot, Zhiheng Pei, Xiang Shu, Fen Wu, Nathaniel Rothman, Jie Wu, Qing Lan, Qiuyin Cai, Wei Zheng, Yu Chen, Xiao-Ou Shu
Summary: The study found an inverse relationship between overall microbial richness in the oral microbiome and gastric cancer risk. Specific microbial taxa, gene families, and metabolic pathways were associated with gastric cancer risk. The results suggest that the oral microbiota may play a role in the etiology of gastric cancer.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Agriculture, Dairy & Animal Science
Sungho Do, Liz Koutsos, Pamela L. Utterback, Carl M. Parsons, Maria R. C. de Godoy, Kelly S. Swanson
JOURNAL OF ANIMAL SCIENCE
(2020)
Article
Nutrition & Dietetics
Matthew Harrison, Gaelle Thomas, Matthew Gilham, Kerry Gray, Alison Colyer, David Allaway
BRITISH JOURNAL OF NUTRITION
(2020)
Article
Agriculture, Dairy & Animal Science
Gloria A. Casas, Laia Blavi, Tzu-Wen L. Cross, Anne H. Lee, Kelly S. Swanson, Hans H. Stein
JOURNAL OF ANIMAL SCIENCE
(2020)
Article
Agriculture, Dairy & Animal Science
Julia Guazzelli Pezzali, Heather L. Acuff, Will Henry, Celeste Alexander, Kelly S. Swanson, Charles G. Aldrich
JOURNAL OF ANIMAL SCIENCE
(2020)
Article
Biotechnology & Applied Microbiology
David Allaway, Richard Haydock, Zoe N. Lonsdale, Oliver D. Deusch, Ciaran O'Flynn, Kevin R. Hughes
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Agriculture, Dairy & Animal Science
James R. Templeman, Emma Thornton, Cara Cargo-Froom, Eli J. Squires, Kelly S. Swanson, Anna K. Shoveller
JOURNAL OF ANIMAL SCIENCE
(2020)
Article
Veterinary Sciences
S. Gomart, D. Allaway, M. Harrison, D. Dickson, J. Seo, L. Ferasin, J. R. Payne, M. J. Hezzell, K. Borgeat
JOURNAL OF SMALL ANIMAL PRACTICE
(2020)
Article
Orthopedics
Csaba Matta, Christopher R. Fellows, Helen Quasnichka, Adam Williams, Bernadette Jeremiasse, David Allaway, Ali Mobasheri
Summary: The study implicates the protein clusterin in the catabolic responses of chondrocytes, particularly highlighting the suppressed release of its secreted form after cytokine stimulation, potentially limiting its cytoprotective function. Analysis of equine cartilage explants and osteochondral biopsies confirmed elevated release of MMP-3, MMP-13, COMP, and sGAG following cytokine treatment, indicating cartilage degradation.
JOURNAL OF ORTHOPAEDIC RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Marissa R. Pallotto, Patricia M. Oba, Maria R. C. de Godoy, Kirk L. Pappan, Preston R. Buff, Kelly S. Swanson
Summary: The study utilized metabolomic techniques to analyze the effects of reduced food intake and weight loss in overweight cats, identifying a continual shift in metabolite profile as weight loss progressed. Most lipid metabolites decreased, but ketone bodies and small lipid particles increased with weight loss, while carbohydrate metabolites decreased.
Article
Agriculture, Dairy & Animal Science
Jujhar Atwal, Jonathan Stockman, Matthew Gilham, David Allaway, Helen Renfrew, Anne Marie Bakke, Phillip Watson
Summary: The study examined the effects of a high calcium diet on adult beagles for 40 weeks and found no measurable adverse health effects. This suggests that the consequences of high calcium intake on adult dogs of different breeds and sizes warrant further investigation.
Article
Veterinary Sciences
Anne Marie Bakke, Joshua Wood, Carina Salt, David Allaway, Matt Gilham, Gail Kuhlman, Tiffany Bierer, Richard Butterwick, Ciaran O'Flynn
Summary: The study showed that feeding grain-free diets with high inclusion of split peas and lentils may lead to canine diet-induced dilated cardiomyopathy, and the data will help generate hypotheses for future studies.
BMC VETERINARY RESEARCH
(2022)
Article
Veterinary Sciences
David Allaway, Janet E. Alexander, Laura J. Carvell-Miller, Rhiannon M. Reynolds, Catherine L. Winder, Ralf J. M. Weber, Gavin R. Lloyd, Andrew D. Southam, Warwick B. Dunn
Summary: Biomarker discovery using biobank samples collected from veterinary clinics can provide insights into the diverse population of pets and accelerate diagnostic development. Metabolomics analysis of DBS samples is a valuable approach to detect health/disease phenotypes. The study demonstrates that DBS samples are suitable for biomarker discovery.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Geriatrics & Gerontology
Carina Salt, Emi K. Saito, Ciaran O'Flynn, David Allaway
Summary: Aging is a complex process involving changes in metabolic processes, immune capacities, and genetic/epigenetic repertoires. With exposure to environmental stresses and deterioration of physiological functions, body systems become more susceptible to chronic inflammation and various pathologies. This study used disease diagnosis data from millions of cats and dogs to define adult life stages based on age clusters and disease patterns, providing valuable information for healthcare recommendations.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Patrick C. Barko, Stanley I. Rubin, Kelly S. Swanson, Maureen A. McMichael, Marcella D. Ridgway, David A. Williams
Summary: Exocrine pancreatic insufficiency (EPI) is a digestive disorder in dogs caused by insufficient secretion of digestive enzymes. In this study, untargeted metabolomics analysis was used to identify metabolic disturbances associated with EPI. 114 serum metabolites were found to differ significantly between dogs with EPI and healthy controls, suggesting malnourishment, micronutrient deficiencies, altered gut microbiome composition, and intestinal inflammation in dogs with EPI.
Article
Nutrition & Dietetics
Patricia M. Oba, Hannah D. Holscher, Rose Ann Mathai, Juhee Kim, Kelly S. Swanson