Article
Genetics & Heredity
Rohia Alili, Eugeni Belda, Phuong Le, Thierry Wirth, Jean-Daniel Zucker, Edi Prifti, Karine Clement
Summary: The study introduced a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of the human gut microbiome using Oxford Nanopore sequencing technology. It proposed rapid personalized whole-genome profiling of target microbiome species through simulations and validation with actual samples, providing new insights for the clinical application of gut microbiome analysis technology.
Article
Biotechnology & Applied Microbiology
Veena Gayathri Krishnaswamy, Mariyam Fathima Jaffar, Rajalakshmi Sridharan, Shruthi Ganesh, Suryasri Kalidas, Vignesh Palanisamy, Kabilan Mani
Summary: The study examined the toxicity of pesticide on earthworms and its impact on the gut microbiome, revealing changes in the microbiome after pesticide exposure.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Immunology
Li-Juan Lv, Sheng-Hui Li, Ji-Ying Wen, Guang-Yang Wang, Hui Li, Tian-Wen He, Qing-Bo Lv, Man-Chun Xiao, Hong-Li Duan, Min-Chai Chen, Zhou-Ting Yi, Qiu-Long Yan, Ai-Hua Yin
Summary: This study compared the gut microbiome of patients with preeclampsia (PE) and healthy pregnant women. The results showed that the gut microbiota of PE patients had certain enriched species and microbial functions, while the gut microbiome of healthy pregnant women had different enriched species and functions. The diagnostic potential of gut microbial biomarkers for PE was also developed.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Dalan Jing, Xiaodan Jiang, Xiaotong Ren, Jie Su, Chen Huang, Jiarui Yang, Ran Hao, Xuemin Li
Summary: Using metagenomic nanopore sequencing, we investigated the composition of the ocular microbiome in patients with Meibomian gland dysfunction (MGD). The bacterial composition differed between different severity levels of MGD, with the severe cases having the simplest composition. Metagenomic nanopore sequencing detected more bacterial species compared to traditional culture methods.
FRONTIERS IN MEDICINE
(2022)
Article
Veterinary Sciences
Ling Guo, Dan Zhang, Shulin Fu, Jiacheng Zhang, Xiaofang Zhang, Jing He, Chun Peng, Yunfei Zhang, Yinsheng Qiu, Chun Ye, Yu Liu, Zhongyuan Wu, Chien-An Andy Hu
Summary: The study presented in this paper suggests that colistin may influence pig gut microbiome by increasing microbial diversity, upregulating antibiotic resistance genes, and modulating microbiome composition. Further analysis revealed significant changes in abundance of certain species and impacts on cellular metabolism and signaling pathways after colistin treatment.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Biochemical Research Methods
Zhenmiao Zhang, Chao Yang, Werner Pieter Veldsman, Xiaodong Fang, Lu Zhang
Summary: This paper comprehensively evaluates 19 commonly used assembly tools on metagenomic sequencing datasets from simulation, mock communities, and human gut microbiomes. It finds that long-read assemblers generate high contig contiguity but fail to reveal some medium- and high-quality metagenome-assembled genomes (MAGs). Linked-read assemblers obtain the highest number of overall near-complete MAGs from the human gut microbiomes. Hybrid assemblers using both short- and long-read sequencing are promising methods to improve both total assembly length and the number of near-complete MAGs. The paper also discusses the running time and memory consumption of these assembly tools and provides practical guidance for selecting them.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Yu Shi, Guoping Wang, Harry Cheuk-Hay Lau, Jun Yu
Summary: Whole genome metagenomic sequencing is a powerful technology that allows the identification of all genes from different organisms in a complex sample. However, the presence of excessive host DNA poses a challenge in metagenomic studies, and various methods have been developed to remove host DNA and improve microbial detection sensitivity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Shuwen Han, Jing Zhuang, Yuefen Pan, Wei Wu, Kefeng Ding
Summary: This study found that microbial SNP was the best method to identify CRC, with a higher accuracy than using the gut microbiome.
MICROBIOLOGY SPECTRUM
(2022)
Article
Immunology
Bo Zhang, Matthew Brock, Carlos Arana, Chaitanya Dende, Nicolai Stanislas van Oers, Lora Hooper, Prithvi Raj
Summary: Bead-beating is critical for DNA extraction, influencing the accurate assessment of microbial community composition. Full length 16S rRNA gene sequencing revealed species diversity in mouse and human gut microbiomes, as well as different levels of sensitivity to bead-beating treatment.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Yulan Cai, Yanhong Luo, Ninan Dai, Yan Yang, Ying He, Huajun Chen, Manlu Zhao, Xiaoyun Fu, Tao Chen, Zhouxiong Xing
Summary: Hyperoxia induces dysbiosis in the gut microbiome and disrupts carbohydrate and lipid metabolism. Moreover, it impairs unsaturated fatty acid metabolism in the gut and inhibits HIF-1 and glucagon signaling pathways in the serum.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Xiangning Bai, Aswathy Narayanan, Piotr Nowak, Shilpa Ray, Ujjwal Neogi, Anders Sonnerborg
Summary: The gut microbiome plays a significant role in HIV-1 immunopathogenesis, with HIV-1-infected individuals on ART showing reduced alpha diversity and increased beta diversity compared to HIV-1-negative controls. Specific species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were enriched in the HIV-1-ART group. The degree of immunodeficiency correlated with gut microbiome composition and metabolic pathways, while microbial shifts were associated with changes in virulome and resistome. Methodological evaluations highlighted the impact of DNA extraction protocols on genomic DNA quantity and quality, as well as the importance of metagenome sequencing depth for recovering microbial genes. Less than 5 million reads per sample were found sufficient for taxonomy profiling in human fecal metagenomic samples.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ophthalmology
Wei Xue, Peiyao Peng, Xiaofeng Wen, Huan Meng, Yali Qin, Tingting Deng, Shixin Guo, Tingting Chen, Xifang Li, Juanran Liang, Feng Zhang, Zhi Xie, Ming Jin, Qiaoxing Liang, Lai Wei
Summary: This study investigated the dysbiosis of gut microbiota associated with age-related macular degeneration (AMD) in Chinese and Swiss cohorts. Cross-cohort gut microbial signatures involving bacterial taxa, viral communities, and metabolic pathways associated with AMD were identified, providing potential targets for the prevention and treatment of AMD.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)
Article
Microbiology
Casper S. Poulsen, Claus T. Ekstrom, Frank M. Aarestrup, Sunje J. Pamp
Summary: Metagenomics is increasingly used to describe microbial communities in biological specimens. This study assessed the effect of library preparation kits and DNA sequencing platforms on the inferred microbial community composition. The results showed that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition, with sequencing platforms introducing more variation than library preparation. Therefore, standardization of sample processing is crucial for generating comparable data within a study.
MICROBIOLOGY SPECTRUM
(2022)
Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Article
Genetics & Heredity
Marin Volaric, Damira Veseljak, Brankica Mravinac, Nevenka Mestrovic, Evelin Despot-Slade
Summary: This study optimized the isolation of HMW DNA from the model beetle Tribolium and successfully overcame challenges in HMW handling and library preparation for Nanopore sequencing. Isolation of nuclei and subsequent purification of DNA on an anion-exchange chromatography column resulted in genomic HMW DNA of optimal quality and quantity.
Article
Multidisciplinary Sciences
Jinyuan Yan, Chen Liao, Bradford P. Taylor, Emily Fontana, Luigi A. Amoretti, Roberta J. Wright, Eric R. Littmann, Anqi Dai, Nicholas Waters, Jonathan U. Peled, Ying Taur, Miguel-Angel Perales, Benjamin A. Siranosian, Ami S. Bhatt, Marcel R. M. van den Brink, Eric G. Pamer, Jonas Schluter, Joao B. Xavier
Summary: In this study, we used shotgun metagenomics to analyze the functional level of the gut microbiome in hospitalized patients receiving hematopoietic cell transplants. We compiled a dataset of 395 samples and provided accession numbers for easy analysis in a public repository.
Article
Medicine, Research & Experimental
Christopher J. Severyn, Benjamin A. Siranosian, Sandra Tian-Jiao Kong, Angel Moreno, Michelle M. Li, Nan Chen, Christine N. Duncan, Steven P. Margossian, Leslie E. Lehmann, Shan Sun, Tessa M. Andermann, Olga Birbrayer, Sophie Silverstein, Carol G. Reynolds, Soomin Kim, Niaz Banaei, Jerome Ritz, Anthony A. Fodor, Wendy B. London, Ami S. Bhatt, Jennifer S. Whangbo
Summary: This pilot study examined the impact of gut decontamination (GD) on gut microbiome composition and the incidence of acute graft-versus-host disease (aGVHD) in patients undergoing allogeneic hematopoietic cell transplantation (HCT). The study found that GD did not affect gut microbiome diversity or clinical outcomes, but it may protect against gut-derived bloodstream infections (BSI) by decreasing the prevalence or abundance of gut pathogens.
Article
Biotechnology & Applied Microbiology
Matthew G. Durrant, Alison Fanton, Josh Tycko, Michaela Hinks, Sita S. Chandrasekaran, Nicholas T. Perry, Julia Schaepe, Peter P. Du, Peter Lotfy, Michael C. Bassik, Lacramioara Bintu, Ami S. Bhatt, Patrick D. Hsu
Summary: Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. In this study, a computational approach was developed to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity and enabling more efficient DNA integration. This research provides new tools for inserting large sequences into the human genome.
NATURE BIOTECHNOLOGY
(2023)
Article
Microbiology
Jonas Schluter, Ana Djukovic, Bradford P. Taylor, Jinyuan Yan, Caichen Duan, Grant A. Hussey, Chen Liao, Sneh Sharma, Emily Fontana, Luigi A. Amoretti, Roberta J. Wright, Anqi Dai, Jonathan U. Peled, Ying Taur, Miguel-Angel Perales, Benjamin A. Siranosian, Ami S. Bhatt, Marcel R. M. van den Brink, Eric G. Pamer, Joao B. Xavier
Summary: TaxUMAP is a visualization tool that allows for the display of microbiome states in large clinical datasets. It was used to create a microbiome atlas of 1,870 cancer patients undergoing therapy-induced perturbations. The tool revealed associations between bacterial density, diversity, and antimicrobial resistance genes. It also identified certain species associated with lower risk for bacteremia, validating a competitive interaction. TaxUMAP provides valuable insights into the effects of the microbiome on human health.
CELL HOST & MICROBE
(2023)
Article
Biotechnology & Applied Microbiology
Dylan G. Maghini, Mai Dvorak, Alex Dahlen, Morgan Roos, Scott Kuersten, Ami S. Bhatt
Summary: To accurately measure microbes, it is important to evaluate biases related to sample condition, preservative method, and bioinformatic analyses. Absolute abundance measurements provide more information than relative abundance and can correct conclusions drawn from relative abundance data. This study investigated the impact of different preservatives and storage conditions on microbial measurements. OMNIgene GUT OMR-200 had less taxonomic variation in metagenomic data, while Zymo DNA/RNA Shield had less variation in metatranscriptomic data. Absolute abundance measurements revealed different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. The study recommends using OMNIgene GUT OMR-200 for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and advocates for the use of absolute quantification in microbial measurements.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Yishay Pinto, Meenakshi Chakraborty, Navami Jain, Ami S. Bhatt
Summary: Phanta is a gut microbiome profiling tool that considers the characteristics of viruses and their interactions with other gut microbes, accurately and quickly detecting bacteria and viruses. It overcomes the technical limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and recently published catalogs of gut viral genomes. When applied to fecal metagenomes from 245 healthy adults, Phanta is able to identify approximately 200 viral species per sample, which is 5 times more than standard assembly-based methods.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Laura J. Keller, Taylor H. Nguyen, Lawrence J. Liu, Brianna M. Hurysz, Markus Lakemeyer, Matteo Guerra, Danielle J. Gelsinger, Rachael Chanin, Nhi Ngo, Kenneth M. Lum, Franco Faucher, Phillip Ipock, Micah J. Niphakis, Ami S. Bhatt, Anthony J. O'Donoghue, Kerwyn Casey Huang, Matthew Bogyo
Summary: In this study, serine hydrolases specific to the Bacteroidetes phylum were identified in the gut commensal Bacteroides thetaiotaomicron. Two of them were predicted to be homologs of the human dipeptidyl peptidase 4 (hDPP4). Functional studies showed that BT4193 is a true homolog of hDPP4 and can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other one is a misannotated proline-specific triaminopeptidase. The results also indicated that BT4193 is important for envelope integrity and fitness of B. thetaiotaomicron in a diverse bacterial community, independent of its proteolytic activity.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Medicine, General & Internal
J. Bolanos-Meade, M. Hamadani, J. Wu, M. M. Al Malki, M. J. Martens, L. Runaas, H. Elmariah, A. R. Rezvani, M. Gooptu, K. T. Larkin, B. C. Shaffer, N. El Jurdi, A. W. Loren, M. Solh, A. C. Hall, A. M. Alousi, O. H. Jamy, M. -A. Perales, J. M. Yao, K. Applegate, A. S. Bhatt, L. S. Kean, Y. A. Efebera, R. Reshef, W. Clark, N. L. DiFronzo, E. Leifer, M. M. Horowitz, R. J. Jones, S. G. Holtan
Summary: This study compared the efficacy of two prophylaxis regimens for graft-versus-host disease (GVHD) in patients with hematologic cancers. The results showed that patients receiving cyclophosphamide-tacrolimus-mycophenolate mofetil had significantly higher GVHD-free, relapse-free survival at 1 year compared to those receiving tacrolimus-methotrexate.
NEW ENGLAND JOURNAL OF MEDICINE
(2023)
Article
Oncology
Wayne Wong, James C. Dickerson, Yannis K. Valtis, Marta Habet, Margaret Bernard, Lorna Kelly, John Lattin, Philip Garrity, Rupali Sood, Alec Ohanian, Maryanne W. Chege, Ami S. Bhatt, Franklin W. Huang, Ramon Yacab
Summary: In 2018, the first public oncology clinic was established in Belize. This article reports demographics from the clinic and describes time intervals to care milestones to allow for public health targeting of gaps and provide a roadmap for public cancer care in the country.
Article
Multidisciplinary Sciences
Julia D. Ransohoff, Victor Ritter, Natasha Purington, Karen Andrade, Summer Han, Mina Liu, Su-Ying Liang, Esther M. John, Scarlett L. Gomez, Melinda L. Telli, Lidia Schapira, Haruka Itakura, George W. Sledge, Ami S. Bhatt, Allison W. Kurian
Summary: In this study of 772 women undergoing TNBC therapy, antimicrobial prescription during TNBC treatment was found to be associated with inferior overall and breast cancer-specific survival. This association was related to peripheral lymphocyte count and gut microbiome dysbiosis. The findings suggest that antimicrobial exposure negatively impacts TNBC survival and can inform prescribing decisions in TNBC and other hormone receptor-independent cancers.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Naomi L. Haddock, Layla J. Barkal, Nikhil Ram-Mohan, Gernot Kaber, Charles Y. Chiu, Ami S. Bhatt, Samuel Yang, Paul L. Bollyky
Summary: This study found that bacterial infections release bacteriophage DNA fragments in plasma, which can be used to identify the types and strains of pathogenic bacteria. Additionally, phage sequences can differentiate between pathogenic and contaminant strains of bacterial species such as Escherichia coli and Staphylococcus aureus. Therefore, phage DNA in plasma is of great importance in studying bacterial infections.
NATURE MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Aravind Natarajan, Brayon J. Fremin, Danica T. Schmidtke, Marlene K. Wolfe, Soumaya Zlitni, Katherine E. Graham, Erin F. Brooks, Christopher J. Severyn, Kathleen M. Sakamoto, Norman J. Lacayo, Scott Kuersten, Jeff Koble, Glorianna Caves, Inna Kaplan, Upinder Singh, Prasanna Jagannathan, Andrew R. Rezvani, Ami S. Bhatt, Alexandria B. Boehm
Summary: Microbial source tracking (MST) uses host-associated fecal markers to identify sources of fecal contamination in the environment. We developed and tested novel viral MST markers based on the genomes of tomato brown rugose fruit virus (ToBRFV). These markers are sensitive and specific to human stool and wastewater, and are more prevalent and abundant compared to the commonly used viral marker PMMoV coat protein (CP) gene. This study suggests that ToBRFV is a promising viral human-associated MST marker.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: Structured RNAs play crucial roles in viruses and their interactions with host genes. This study screened over 5 million viral sequences and predicted 10,006 novel candidate structured RNAs, with evidence of transcription in the human fecal microbiome. The findings provide insights into the extensive diversity of structured RNAs in viruses and their implications in viral gene expression.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Oncology
Wayne Wong, James C. Dickerson, Yannis K. Valtis, Marta Habet, Margaret Bernard, Lorna Kelly, John Lattin, Philip Garrity, Rupali Sood, Alec Ohanian, Maryanne W. Chege, Ami S. Bhatt, Franklin W. Huang, Ramon Yacab
Summary: This study reports the first clinic-based cancer statistics for Belize and highlights the long time intervals between symptom onset and treatment for many patients. Despite serving an underserved population, the clinic has built infrastructure to minimize delays in care, emphasizing the importance of infrastructure investment and early detection programs to improve outcomes in Belize.