Article
Microbiology
Koray Ergunay, Mathew Mutinda, Brian Bourke, Silvia A. Justi, Laura Caicedo-Quiroga, Joseph Kamau, Samson Mutura, Irene Karagi Akunda, Elizabeth Cook, Francis Gakuya, Patrick Omondi, Suzan Murray, Dawn Zimmerman, Yvonne-Marie Linton
Summary: This study focused on using ticks as xenosurveillance sentinels to detect circulating pathogens in Kenyan drylands. Host-feeding ticks collected from various wild animals and domestic animals were screened using metagenomics. The results showed that ticks carried a wide range of pathogenic bacteria, viruses, and fungi, with the potential for transmission between wildlife, livestock, and humans in the Kenyan landscape.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yunxi Liu, R. A. Leo Elworth, Michael D. Jochum, Kjersti M. Aagaard, Todd J. Treangen
Summary: Contaminant sequences in metagenomic samples can impact interpretation of microbiome studies, especially in low biomass environments. The authors propose a computational approach called Squeegee, which can detect microbial contamination and identify contaminants in publicly available datasets lacking negative controls.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Pengshuo Yang, Xue Zhu, Kang Ning
Summary: Microbes in different habitats exhibit specific species and gene enrichment patterns, reflecting the biome-species-function relationship influenced by ecological and evolutionary principles. However, a comprehensive understanding of these patterns and the driving factors behind them remains limited. In this study, enrichment patterns were examined in 1705 microbiome samples from four representative biomes, and an enrichment sphere model was constructed to reveal the regulatory principles. Case studies demonstrated the enrichment of copper-resistance genes in soil biomes due to contamination and horizontal gene transfer, and the enrichment of flagellum-related genes in freshwater biomes due to fluidity and vertical gene accumulation. The enrichment sphere model has practical applications in biome identification and protein structure modeling. Overall, the model aims to provide a comprehensive understanding of the biome-species-function relationships.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Byunghan Lee, Hyeyoung Min, Sungroh Yoon, Inanc Birol
Summary: This study proposes an efficient method for error correction in metagenomic sequencing, reducing denoising time demands and overestimation of OTUs. By utilizing data-level parallelism and multiple processing units, the approach significantly improves the efficiency of denoising efforts and provides web-based visualization of results.
Article
Multidisciplinary Sciences
Hyunmin Koo, Casey D. Morrow
Summary: This study developed an analytic method to detect indicators of microbial strain dysbiosis and found shared gut commensal microbes in both healthy individuals and COVID-19 patients, suggesting a potential dysbiosis in the microbial strain community.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Samuel Zimmerman, Braden T. Tierney, Chirag J. Patel, Aleksandar D. Kostic
Summary: This study quantified the heterogeneity in microbial gene content across different ecological environments. The researchers identified a large number of nonredundant genes, with the majority occurring in only one sample. They also discovered sets of genes associated with specific ecological environments and highlighted the incompleteness and inaccuracy of previous microbiome gene catalogs.
Article
Chemistry, Physical
Maxime Blatter, Louis Delabays, Clement Furrer, Gerald Huguenin, Christian Pierre Cachelin, Fabian Fischer
Summary: The construction and long-term reliability of large microbial fuel cells (MFCs) are current challenges. Research has shown that MFCs can effectively remove pollutants such as COD, ammonia, and phosphorus from wastewater under specific conditions, while also achieving energy self-sufficiency.
JOURNAL OF POWER SOURCES
(2021)
Article
Microbiology
Lingdi Zhang, Jahan Rahman, Matthew Chung, Lauren Lashua, Aubree Gordon, Angel Balmaseda, Guillermina Kuan, Richard Bonneau, Elodie Ghedin
Summary: Based on the analysis of household samples, we found that metagenomic-type analyses of the microbiome can track the transmission of airway bacteria. Microbial communities were more similar between individuals who cohabit in the same household than between individuals from different households. Sharing of bacteria from the airways increased in households with influenza infections compared to control households. However, due to the limited number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.
Article
Microbiology
Carl-Eric Wegner, Raphaela Stahl, Irina Velsko, Alex Huebner, Zandra Fagernaes, Christina Warinner, Robert Lehmann, Thomas Ritschel, Kai U. Totsche, Kirsten Kuesel
Summary: By adapting methods from microbial archaeology and paleogenomics, we recovered sufficient DNA from seven rock specimens for metagenomic analysis. Limestones serve as archives for genetic records of past microbial communities, including those sensitive to environmental stress, due to specific conditions facilitating long-term DNA preservation.
Article
Environmental Sciences
Hannah C. Lepper, Meghan R. Perry, Bryan A. Wee, David Wills, Hanne Nielsen, Saria Otani, Moray Simon, Frank M. Aarestrup, Mark E. J. Woolhouse, Bram A. D. van Bunnik
Summary: This study compares the resistome and microbiome of hospital, community, and mixed municipal wastewater and finds that the resistome in hospital wastewater is different from that in other locations.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Joanna Coker, Kateryna Zhalnina, Clarisse Marotz, Deepan Thiruppathy, Megan Tjuanta, Gavin D'Elia, Rodas Hailu, Talon Mahosky, Meagan Rowan, Trent R. Northen, Karsten Zengler
Summary: Microbes and plants form beneficial associations in soil communities, contributing to the growth and health of both. This study develops a model synthetic community of 16 soil microorganisms to advance research on plant-microbe interactions. The optimized preservation and dissemination methods of this microbial community will enhance soil microbe research.
Article
Agricultural Engineering
Nathan Innard, James P. J. Chong
Summary: Mixed anaerobic microbial communities play a key role in valorizing waste biomass through anaerobic digestion, and are important in soil and animal microbiomes. Understanding interactions between individual species within these communities is crucial for improving the performance and potential applications of green technology. The challenges associated with assessing the status of anaerobic microbial communities, incorporating measurements into control philosophies, and enhancing their potential to produce higher value products from waste materials are discussed.
BIORESOURCE TECHNOLOGY
(2022)
Review
Engineering, Marine
Cora Hoerstmann, Sylke Wohlrab, Uwe John
Summary: High-throughput sequencing technologies have advanced our understanding of microbial diversity in the oceans, but research on microbial eukaryotes (protists) lags behind. This review discusses the challenges and opportunities of high-throughput sequencing methods for studying the evolutionary, ecological, and functional aspects of oceanic protists. These approaches allow for a deeper understanding of the functional role of protists and the changes in marine ecosystems.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Review
Chemistry, Multidisciplinary
Zhenyu Yang, Ping Li, Wei Feng, Yu Chen
Summary: Oxygen is crucial for regulating metabolic activities in living organisms, but disease-induced hypoxia reduces the effectiveness of various therapies. Nanomaterials with oxygen-production capacity have been developed to recover oxygen function in tissue, but there are limitations. Photosynthetic microorganisms have efficient photocatalytic oxygen production efficacy and desirable biocompatibility, making them extensively applied for improving hypoxia in diseases. This review summarizes the research progress on microbial-based photosynthetic oxygenation in cancer therapy, wound healing, and tissue engineering, emphasizing the importance of biocompatibility in vivo and discussing the future evolution of microbial-based treatment.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Microbiology
Siew Herng Chan, Muhammad Hafiz Ismail, Chuan Hao Tan, Scott A. Rice, Diane McDougald
Summary: The study found that predation by protozoa and bacteriophage positively correlated with the formation of aerobic granules. The increase in abundance of filamentous phages may promote the structural formation of granules, while the absence of protozoa after chemical treatment delayed the initiation of granules formation.
Article
Public, Environmental & Occupational Health
Liang En Wee, Edwin Philip Conceicao, Jean Xiang-Ying Sim, May Kyawt Aung, Myat Oo Aung, Yang Yong, Shalvi Arora, Karrie Kwan-Ki Ko, Indumathi Venkatachalam
Summary: Sporadic clusters of COVID-19 infection occurred in a highly vaccinated health care workers and patient population, despite enhanced infection-prevention measures. The unvaccinated and immunocompromised individuals remain at risk and should receive enhanced surveillance.
AMERICAN JOURNAL OF INFECTION CONTROL
(2022)
Article
Chemistry, Analytical
Danny Jian Hang Tng, Bryan Chu Yang Yin, Jing Cao, Kwan Ki Karrie Ko, Kenneth Choon Meng Goh, Delia Xue Wen Chua, Yong Zhang, Melvin Lee Kiang Chua, Jenny Guek Hong Low, Eng Eong Ooi, Khee Chee Soo
Summary: This study reports an Amplified Parallel ART (AP-ART) that can quickly detect the COVID-19 virus with high sensitivity, even when using non-fasted saliva samples. Compared to existing techniques, AP-ART achieved a lower limit of detection. This new method has the potential to be used for rapid testing in resource-limited settings and play a crucial role in early diagnosis.
Article
Microbiology
Karrie K. K. Ko, Nurdyana Binte Abdul Rahman, Shireen Yan Ling Tan, Kenneth X. L. Chan, Sui Sin Goh, James Heng Chiak Sim, Kun Lee Lim, Wan Loo Tan, Kian Sing Chan, Lynette L. E. Oon, Niranjan Nagarajan, Chayaporn Suphavilai
Summary: This study reveals a previously unreported mutation in the N gene of SARS-CoV-2, which may render certain commercial tests unable to accurately detect the virus, highlighting the importance of real-time surveillance of viral variants.
MICROBIOLOGY SPECTRUM
(2022)
Editorial Material
Medicine, General & Internal
Liang En Wee, Ai Ling Tan, Siang Hui Lai, Karrie Kwan-Ki Ko, Ing Xiang Soo, Jenny Guek-Hong Low
ANNALS ACADEMY OF MEDICINE SINGAPORE
(2022)
Letter
Immunology
Liang En Wee, Karrie Kwan Ki Ko, Edwin Philip Conceicao, May Kyawt Aung, Myat Oo Aung, Yong Yang, Shalvi Arora, Indumathi Venkatachalam
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Public, Environmental & Occupational Health
Indumathi Venkatachalam, Molly Kue Bien How, Karrie Kwan Ki Ko, Nurdyana Binte Abdul Rahman, Edwin Philip Conceicao, May Kyawt Aung, Myat Oo Aung, Yong Yang, Kwee Yuen Tan, Jean Xiang Ying Sim, Lai Chee Lee, Moi Lin Ling
Summary: This study describes OXA-48-like carbapenem-producing Enterobacteriaceae (CPE) outbreaks at Singapore General Hospital between 2018 and 2020 and identifies the risk factors associated with OXA-48 carriage in the 2020 outbreak. The results indicate that diarrhea, contact with OXA-48-carrying patients, and exposure to carbapenems or penicillin are independent risk factors for OXA-48 carriage. These outbreaks are likely related to favorable ecological conditions and selective pressure from antimicrobial use.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Liang En Wee, Karrie Kwan-Ki Ko, Edwin Philip Conceicao, Jean Xiang-Ying Sim, Nurdyana Abdul Rahman, Shireen Yan-Ling Tan, Delphine Yan-Hong Cao, Kenneth Xing-Long Chan, May Kyawt Aung, Myat Oo Aung, Yang Yong, Shalvi Arora, Molly Kue Bien How, Kwee Yuen Tan, Lai Chee Lee, Thuan Tong Tan, Limin Wijaya, James Heng Chiak Sim, Chayaporn Suphavilai, Indumathi Venkatachalam, Moi Lin Ling
Summary: Despite rigorous surveillance and a highly vaccinated healthcare worker population, sporadic clusters of healthcare-associated COVID-19 occurred during a community surge of the Delta variant. Genomic analysis played a critical role in timely cluster detection and identifying linkages among healthcare workers moving between clinical areas and sharing common lunch areas.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Letter
Public, Environmental & Occupational Health
Liang En Ian Wee, Karrie Kwan-Ki Ko, Edwin Philip Conceicao, May Kyawt Aung, Aung Myat Oo, Yong Yang, Shalvi Arora, Indumathi Venkatachalam
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Letter
Public, Environmental & Occupational Health
Liang En Ian Wee, Karrie Kwan-Ki Ko, Edwin Philip Conceicao, May Kyawt Aung, Myat Oo Aung, Yong Yang, Shalvi Arora, Chayaporn Suphavilai, Indumathi Venkatachalam
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Liang En Wee, Shalvi Arora, Karrie Kwan-Ki Ko, Edwin Philip Conceicao, Kristen K. Coleman, Kwee Yuen Tan, Hatijah Binti Tohid, Qinnan Liu, Grace Li Teng Tung, Shawn Wee Jin See, Chayaporn Suphavilai, Moi Lin Ling, Indumathi Venkatachalam
Summary: This study investigated the contamination of environmental samples in temporary isolation wards converted from general wards or prefabricated containers, and utilized whole-genome sequencing to investigate cluster outbreaks. The results showed environmental contamination with SARS-CoV-2 in temporary isolation wards, mainly from the toilet area and smartphones used for patient communication. However, no healthcare-associated transmission was detected in temporary isolation wards during the entire pandemic period.
AMERICAN JOURNAL OF INFECTION CONTROL
(2023)
Article
Biochemistry & Molecular Biology
Hatairat Yingtaweesittikul, Jiaxi Wu, Aanchal Mongia, Rafael Peres, Karrie Ko, Niranjan Nagarajan, Chayaporn Suphavilai
Summary: The development of CREAMMIST, an integrative database for cancer drug response, allows researchers to capture uncertainty and utilize available data for downstream analyses, providing valuable insights for cancer pharmacogenomics research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Cedric C. S. Tan, Karrie K. K. Ko, Hui Chen, Jianjun Liu, Marie Loh, Minghao Chia, Niranjan Nagarajan
Summary: A large-scale population study reveals that there is no consistent core blood microbiome in healthy individuals. While human blood is generally considered sterile, recent research suggests the presence of a blood microbiome in healthy people. After analyzing sequencing data from multiple cohorts, researchers identified 117 microbial species in the blood of 9,770 healthy individuals, primarily commensals associated with the gut, mouth, and genitourinary tract. However, no co-occurrence patterns or associations between host phenotypes and microbes were found, suggesting that the translocation of commensal microbes from other body sites into the bloodstream is transient and sporadic.
NATURE MICROBIOLOGY
(2023)
Article
Infectious Diseases
Liang En Wee, Jing Yuan Tan, Karrie Kwan-Ki Ko, Wei Yee Wan, Deborah Chooi Mun Lai, Lynette Lin Ean Oon, Alfonso Tan-Garcia, Joe Poh Sheng Yeong, Angela Maria Takano Pena, Tony Kiat Hon Lim, Edwin Philip Conceicao, Indumathi Venkatachalam, Limin Wijaya, Thuan Tong Tan
Summary: This study describes two cases of occult COVID-19 in immunocompromised patients who had previously received rituximab treatment. Lung imaging showed ground-glass infiltrates, but nasopharyngeal samples were negative for SARS-CoV-2, leading to initially ruling out COVID-19. However, bronchoalveolar lavage specimens confirmed the persistence of SARS-CoV-2 in lung parenchyma, and viral isolation and immunohistochemistry further supported ongoing viral persistence and replication.