Article
Engineering, Environmental
Hongsong Liu, Xiao Li, Haojun Lei, Dan Li, Hongxing Chen, Daniel Schlenk, Bo Yan, Luo Yongju, Lingtian Xie
Summary: Excess dietary seleno-L-methionine adversely affects Japanese medaka by inhibiting growth, causing histopathological damage to the gastrointestinal tract, and altering microbial community composition.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Review
Microbiology
Yumeng Wang, Shixi Xu, Qiurong He, Kun Sun, Xiaowan Wang, Xiaorui Zhang, Yuqing Li, Jumei Zeng
Summary: This study evaluates the connection between GI tract biofilms and chronic mucosa diseases such as chronic gastritis, inflammatory bowel disease, and colorectal cancer. The representative biofilm makers including Helicobacter pylori, adherent-invasive Escherichia coli, Bacteroides fragilis, and Fusobacterium nucleatum in each disease are summarized. The study discusses the role of biofilms in causing inflammation and the pro-carcinogenic stage, as well as the typical resistance, persistence, and recurrence mechanisms seen in vitro. Biofilms may serve as a new biomarker for endoscopic and pathologic detection of gastrointestinal disease and suppression, which may be a useful addition to the present therapy strategy.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
H. Panwar, N. Rokana, S. V. Aparna, J. Kaur, A. Singh, J. Singh, K. S. Singh, V. Chaudhary, A. K. Puniya
Summary: The human gastrointestinal tract maintains a unique environment with various defense strategies to restrict the colonization and growth of unfriendly microbial strains, serving as a balance between resident and uninvited organisms. The ability to survive this innate defense mechanism determines the capability of probiotic or pathogen strains to confer health benefits or induce clinical events.
JOURNAL OF APPLIED MICROBIOLOGY
(2021)
Article
Microbiology
Sundas Rani, Martin Tang Sorensen, Jordi Estelle, Samantha Joan Noel, Natalja Norskov, Uffe Krogh, Leslie Foldager, Ole Hojberg
Summary: Glyphosate residues can be found in feed made from genetically modified glyphosate-resistant crops or from conventional crops desiccated with glyphosate before harvest. The present study investigated the potential effects of feed glyphosate on the gastrointestinal microbial ecology of weaned piglets.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agriculture, Dairy & Animal Science
Kai Wang, Hailiang Zhang, Lirong Hu, Guoxing Zhang, Haibo Lu, Hanpeng Luo, Shanjiang Zhao, Huabin Zhu, Yachun Wang
Summary: In this study, the gastrointestinal microbiota of Simmental x Holstein crossbred cattle was investigated. The results showed spatial heterogeneity of the microbiota across different regions of the gastrointestinal tract, with specific microbial biomarkers identified in each region. These findings are important for studying the gastrointestinal microbiome in bovines.
Article
Food Science & Technology
Xinmiao Wang, Qian Wang, Yuanyuan Hu, Fawen Yin, Xiaoyang Liu, Dayong Zhou
Summary: Phenolipids like alkyl gallates (A-GAs) have been approved as non-toxic antioxidant additives in the food industry and are considered a potential source of functional food ingredients. A study using live mice and anaerobic fermentation models showed that A-GAs can be hydrolyzed by intestinal lipases and gut microorganisms to produce free gallic acid (GA). The length of the lipid chain in A-GAs can be adjusted to achieve sustained and controllable release of GA. Furthermore, A-GAs can reach the colon and cecum, potentially providing gastrointestinal protective effects. Therefore, A-GAs may be applied as functional food ingredients.
Article
Environmental Sciences
Anne-Cathrine Storgaard Danielsen, Per Halkjaer Nielsen, Cecilie Hermansen, Peter Lystbaek Weber, Lis Wollesen de Jonge, Vibeke Rudkjobing Jorgensen, Mogens Humlekrog Greve, Derek Corcoran, Morten Kam Dahl Dueholm, Dan Bruhn
Summary: Soils host diverse microbial communities that are essential for ecosystem functions and soil health. However, legislation protecting biodiversity or habitats does not currently cover microorganisms. Recent studies have shown that microbial communities are habitat-specific, suggesting the potential for their inclusion in habitat conservation monitoring. This study examined bacterial and plant communities across different habitat types defined in the Habitats Directive, and identified physico-chemical properties that explain variations in community composition.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Microbiology
Minjuan Li, Dantong Shao, Jiachen Zhou, Jianhua Gu, Junjie Qin, Xinqing Li, Changqing Hao, Wenqiang Wei
Summary: Upper gastrointestinal (UGI) tract cancer is one of the most common cancers worldwide, but the UGI microbiota has received limited attention. This study revealed that each gastrointestinal site has its own microbial characteristics that overlap those of adjacent sites. The microbial compositions between the UGI sites and feces showed significant differences. Helicobacter pylori played a more significant role in the microbial composition of the noncardia stomach than in that of the cardia. Gastric pH and Helicobacter pylori had similar additive effects on the microbial diversity of gastric juice.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biotechnology & Applied Microbiology
Yixiao Zhu, Zhisheng Wang, Rui Hu, Xueying Wang, Fengpeng Li, Xiangfei Zhang, Huawei Zou, Quanhui Peng, Bai Xue, Lizhi Wang
Summary: Investigating the gastrointestinal bacterial communities in Xuanhan yellow cattle and Simmental crossbred cattle revealed differences in diversity, structure, and composition among different gastrointestinal regions, with the rumen exhibiting more stability characteristics. Despite breed differences, the composition and structure of the bacterial communities in the rumen, small intestine, and large intestine were distinct, suggesting potential implications for gut-microbe interactions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Environmental Sciences
Ting Wang, Xiaoshang Ru, Beini Deng, Chenxi Zhang, Xu Wang, Bo Yang, Libin Zhang
Summary: This study investigated the characteristics of marine sediments under a wind farm in China and found that copper, chromium, and zinc were the major contaminants. The pollution level in the wind farm was relatively light compared to baseline values. The physicochemical features of the sediments explained the changes in microorganisms, and the relative abundance of microorganisms correlated with sediment quality. This comprehensive study fills a knowledge gap and enhances our understanding of assessing sedimentary environments in offshore wind farms.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Marine & Freshwater Biology
Zoe A. A. Pratte, Frank J. J. Stewart, Christina A. A. Kellogg
Summary: Using the GeoChip 5.0S microarray, a functional gene study of microbiomes from five species of cold-water corals was conducted, revealing functional differences and similarities among the different species. The microbiomes of Acanthogorgia spp. were the most distinct and least diverse, while Desmophyllum spp. were more similar to each other. Only 7 out of 59 metabolic sub-categories showed notable differences between deep-water and tropical corals.
Article
Multidisciplinary Sciences
Samantha J. Monohon, Daniel K. Manter, Jorge M. Vivanco
Summary: The conditioning of microbial communities related to disease resistance over generations can lead to the development of suppressive soils for plant defense responses. However, conditioning soils for drought resistance resulted in significantly decreased plant biomass in two generations of growth.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Danyan Qiu, Nuohan Xu, Qi Zhang, Wenya Zhou, Yan Wang, Zhenyan Zhang, Yitian Yu, Tao Lu, Liwei Sun, Ning-Yi Zhou, W. J. G. M. Peijnenburg, Haifeng Qian
Summary: This study assessed the effects of abamectin on soil microorganisms by treating plant-soil microcosms with abamectin at concentrations of 0.1 and 1.0 mg/kg. The results showed that although abamectin was degradable, it altered soil microbial communities, disrupted microbial interactions, and decreased community complexity and stability. At the higher concentration, opportunistic human diseases and soil-borne pathogens were enriched in the soil. However, most ecological functions in the soil recovered within 21 days after abamectin treatment.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Animesh Anand Mishra, Andrew Y. Koh
Summary: Candida species, especially Candida albicans, are prevalent and abundant members of the gut mycobiota. In a healthy host, Candida albicans exists as a pathobiont in a commensal state but can become pathogenic when the host's immune system is suppressed. The factors determining Candida's colonization and dissemination in mucosal surfaces remain of great interest for further research.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Engineering, Environmental
Stephanie L. Rich, Michael T. Zumstein, Damian E. Helbling
Summary: The research aimed to identify functional groups that influence rates of micropollutant biotransformation in wastewater microbial communities. Through incubation experiments and random forest models, 30 functional groups were classified as biotransformation promoters, inhibitors, features that can be transformed, or features that are not rate-determining, providing new insights for predicting micropollutant biotransformations and designing more biodegradable chemical products for wastewater treatment.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Microbiology
Caisey V. Pulford, Blanca M. Perez-Sepulveda, Rocio Canals, Jessica A. Bevington, Rebecca J. Bengtsson, Nicolas Wenner, Ella V. Rodwell, Benjamin Kumwenda, Xiaojun Zhu, Rebecca J. Bennett, George E. Stenhouse, P. Malaka De Silva, Hermione J. Webster, Jose A. Bengoechea, Amy Dumigan, Alicia Tran-Dien, Reenesh Prakash, Happy C. Banda, Lovemore Alufandika, Mike P. Mautanga, Arthur Bowers-Barnard, Alexandra Y. Beliavskaia, Alexander V. Predeus, Will P. M. Rowe, Alistair C. Darby, Neil Hall, Francois-Xavier Weill, Melita A. Gordon, Nicholas A. Feasey, Kate S. Baker, Jay C. D. Hinton
Summary: This study identified a new lineage of nontyphoidal Salmonella, ST313 L3, which emerged in Malawi in 2016 and is closely related to variants causing gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, a phenomenon not seen in other ST313 lineages.
NATURE MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Angharad E. Green, Deborah Howarth, Chrispin Chaguza, Haley Echlin, R. Fredi Langendonk, Connor Munro, Thomas E. Barton, Jay C. D. Hinton, Stephen D. Bentley, Jason W. Rosch, Daniel R. Neill
Summary: The study investigated the adaptation and evolution of pneumococcus in different transmission environments. Through serial passage experiments in mouse models, pneumococci passaged in the lungs became more effective colonizers of the respiratory tract, displaying potential parallel evolution. Mutations in specific genes were identified in nasopharynx-passaged pneumococci, highlighting the impact of within-host environmental conditions on bacterial evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Virology
Ella V. Rodwell, Nicolas Wenner, Caisey V. Pulford, Yueyi Cai, Arthur Bowers-Barnard, Alison Beckett, Jonathan Rigby, David M. Picton, Tim R. Blower, Nicholas A. Feasey, Jay C. D. Hinton, Blanca M. Perez-Sepulveda
Summary: This study isolated and characterized 32 phages capable of infecting S. Typhimurium and S. Enteritidis from water sources in Malawi and the UK, finding them classified into three major phylogenetic clusters with different geographical distributions and host ranges. Cluster 3, with its 3.b sub-cluster, contained the most novel isolates, representing the first exploration of phages' potential to target the lineages of Salmonella responsible for bloodstream infections in Sub-Saharan Africa.
Article
Biochemistry & Molecular Biology
Youssef El Mouali, Falk Ponath, Vinzent Scharrer, Nicolas Wenner, Jay C. D. Hinton, Joerg Vogel
Summary: ProQ, a FinO-domain protein, is an RNA-binding protein involved in gene regulation in bacterial chromosomes and mobile elements. Mutations in both the FinO domain and the carboxy-terminal region of ProQ have been identified to be critical for its activity, with alterations in the FinO domain leading to rapid turnover of ProQ by the AAA+ family protease Lon. This connects Lon with RNA-dependent quality control of major sRNA chaperones Hfq and ProQ in Gram-negative bacteria.
Article
Microbiology
TuShun R. Powers, Amanda L. Haeberle, Alexander V. Predeus, Disa L. Hammarlof, Jennifer A. Cundiff, Zeus Saldana-Ahuactzi, Karsten Hokamp, Jay C. D. Hinton, Leigh A. Knodler
Summary: The study identified niche-specific bacterial expression profiles and required genes for cytosolic colonization by exploiting the parallel intracellular lifestyles of Salmonella enterica in epithelial cells. It revealed that Salmonella encounters oxidative stress and mineral deprivation in different intracellular compartments, and requires extensive transcriptional reprogramming for successful colonization. Unique virulence gene programs tailored for residence within distinct intracellular compartments were also highlighted.
Article
Microbiology
Sian Owen, Nicolas Wenner, Charles L. Dulberger, Ella Rodwell, Arthur Bowers-Barnard, Natalia Quinones-Olvera, Daniel J. Rigden, Eric J. Rubin, Ethan C. Garner, Michael Baym, Jay C. D. Hinton
Summary: The research identified a family of prophage-encoded phage-defense proteins called BstA in diverse Gram-negative bacteria. BstA protein localizes to sites of exogenous phage DNA replication and mediates abortive infection to suppress competing phage epidemic. It allows prophages to defend host cells against exogenous phage attack without affecting lytic replication.
CELL HOST & MICROBE
(2021)
Article
Biochemistry & Molecular Biology
David M. Picton, Joshua D. Harling-Lee, Samuel J. Duffner, Sam C. Went, Richard D. Morgan, Jay C. D. Hinton, Tim R. Blower
Summary: This study identifies a novel transcriptional regulator, BrxR, and investigates its repressor role in bacterial phage defense systems. Structural analysis and bioinformatic analysis reveal the widespread presence of BrxR in bacteria and its co-localization with various phage defense systems.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Mengru Yang, Nicolas Wenner, Gregory Dykes, Yan Li, Xiaojun Zhu, Yaqi Sun, Fang Huang, Jay C. D. Hinton, Lu-Ning Liu
Summary: This study investigates the de novo biogenesis of Pdu metabolosomes in bacteria and characterizes the roles of key constituents in the formation and positioning of functional metabolosomes. The results show that Pdu metabolosomes undertake both Shell first and Cargo first assembly pathways, and the internal cargo core is formed through ordered assembly of multiple enzyme complexes, exhibiting liquid-like properties.
NATURE COMMUNICATIONS
(2022)
Article
Infectious Diseases
Leonard Koolman, Reenesh Prakash, Yohane Diness, Chisomo Msefula, Tonney S. Nyirenda, Franziska Olgemoeller, Paul Wigley, Blanca Perez-Sepulveda, Jay C. D. Hinton, Sian V. Owen, Nicholas A. Feasey, Philip M. Ashton, Melita A. Gordon
Summary: The study suggests that invasive Salmonella infections in Sub-Saharan Africa are likely transmitted from person to person, rather than through animals or the environment. The diversity of NTS strains found in household environments demonstrates the robustness of NTS sampling and culture methodology.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Microbiology
Sarah Gallichan, Blanca M. Perez-Sepulveda, Nicholas A. Feasey, Jay C. D. Hinton, Juno Thomas, Anthony Marius Smith
Summary: We report a sensitive, time- and cost-effective real-time PCR assay capable of differentiating between different clades of Salmonella enterica serovar Enteritidis. This assay can facilitate surveillance and inform public health responses.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Nancy Yaneth Florez-Delgado, Elizabeth Noelia Ubillus, Blanca Perez-Sepulveda, Eyda Lizeth Ospina-Rios, Ana Karina Carrascal-Camacho, Iliana C. Chamorro-Tobar, Lucy Angeline Montano, Yan Li, Silvana Zapata-Bedoya, Jay C. D. Hinton, Jose Miguel Villarreal, Magdalena Wiesner
Summary: This study analyzed 442 isolates of S. Typhimurium and found that 39% of human clinical isolates and 22% of swine isolates carried complete class 1 integrons. The isolates carrying class 1 integrons were resistant to multiple antimicrobial drugs.
JOURNAL OF MEDICAL MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Wai Yee Fong, Rocio Canals, Alexander Predeus, Blanca Perez-Sepulveda, Nicolas Wenner, Lizeth Lacharme- Lora, Nicholas Feasey, Paul Wigley, Jay C. D. Hinton
Summary: Salmonella enterica Enteritidis is a common serovar of invasive non-typhoidal Salmonella disease in sub-Saharan Africa. The African S. enterica Enteritidis clades have unique genetic signatures and exhibit multi-drug resistance. However, the molecular basis for their enhanced propensity to cause bloodstream infection is not well understood. Using transposon insertion sequencing, the researchers identified genes required for growth and survival in vitro as well as in murine macrophages. These findings provide insights into the virulence factors of African S. enterica Enteritidis.
MICROBIAL GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Sanne Wolput, Angela Makumi, Laura Wicke, Leonard E. Baecker, William Cenens, Yves Briers, Nicolas A. Wenner, Sian V. Owen, Jay C. D. Hinton, Rob Lavigne, Abram Aertsen
Summary: Many phage genes, called ORFans, have no similarity to other genes in current databases. These ORFan genes can have a significant impact on phage propagation and host interactions, but are often unexplored in experiments. In a previous study, we discovered a novel interaction between phage P22 and its host Salmonella Typhimurium, involving the ORFan gene pid. The pid gene is highly expressed in phage carrier cells that harbor a polarly located P22 episome, which segregates unequally among daughter cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Blanca M. Perez-Sepulveda, Darren Heavens, Caisey Pulford, Alexander Predeus, Ross Low, Hermione Webster, Gregory F. Dykes, Christian Schudoma, Will Rowe, James Lipscombe, Chris Watkins, Benjamin Kumwenda, Neil Shearer, Karl Costigan, Kate S. Baker, Nicholas A. Feasey, Jay C. D. Hinton, Neil Hall
Summary: An efficient and cost-effective pipeline has been developed for large-scale collection and genome sequencing of bacterial isolates. Through a worldwide collaboration, over 10,000 diverse isolates of Salmonella enterica were collected and sequenced at a reagent cost of less than USD$10 per genome. This method is applicable to other large bacterial collections to support global collaborations.
Article
Microbiology
Blanca M. Perez-Sepulveda, Alexander Predeus, Wai Yee Fong, Christopher M. Parry, John Cheesbrough, Paul Wigley, Nicholas A. Feasey, Jay C. D. Hinton
Summary: This study presents the complete genome sequencing and annotation of four isolates of Salmonella enterica serovar Enteritidis, representing the Central/Eastern African Glade and the Global Epidemic Glade.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)