Review
Biology
Xia Meng, Mengping He, Pengpeng Xia, Jinqiu Wang, Heng Wang, Guoqiang Zhu
Summary: This article reviews the functions of sRNAs during Salmonella infection of host cells. sRNAs play important roles in helping Salmonella resist acidic environmental stress, regulate virulent genes for adhesion and invasion, adapt to oxidative stress within host cells, and promote survival within macrophages. By regulating gene expression, sRNAs contribute to the pathogenic mechanism of Salmonella.
Review
Immunology
Boris Vidal-Veuthey, Damariz Gonzalez, Juan P. Cardenas
Summary: This article reviews the literature on the functions of secreted proteins from the gut microbiota and discusses their impact on host physiology and health, as well as how these effects can be utilized for the development of postbiotic products.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Gastroenterology & Hepatology
Neelu Begum, Azadeh Harzandi, Sunjae Lee, Mathias Uhlen, David L. Moyes, Saeed Shoaie
Summary: Fungal communities play a crucial role in maintaining the balance of microbial communities and the health of the host, and may influence the development of metabolic diseases and cancer. Studying the metabolic interactions between fungal communities, hosts, and other microorganisms is essential for understanding human diseases.
Review
Immunology
Pilar Cornejo Ulloa, Bastiaan P. Krom, Monique H. van der Veen
Summary: Sex steroid hormones can affect both oral microbiota and host cells, potentially leading to oral health problems. Current research mainly focuses on the impact of hormonal changes on oral microorganisms, while broader studies have suggested new hypotheses about the effects of SSH.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Immunology
Samantha Franklin, Samuel L. Aitken, Yushi Shi, Pranoti V. Sahasrabhojane, Sarah Robinson, Christine B. Peterson, Naval Daver, Nadim A. Ajami, Dimitrios P. Kontoyiannis, Samuel A. Shelburne, Jessica Galloway-Pena
Summary: Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. This study analyzed samples from acute myeloid leukemia patients undergoing induction chemotherapy to characterize the phenomenon of oral-fecal microbiome community coalescence and its clinical implications. The results showed that oral-stool community coalescence was associated with increased risk of infections and specific antimicrobial effects on microbial ecology.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Allan Radaic, Yvonne L. Kapila
Summary: The oralome is a summary of the interactions between oral microorganisms and the host, which can impact the health and disease status of the host. Current research focuses on changes in the oral microbiome in the oral environment and discusses techniques for modulating the dysbiotic oral microbiome to prevent and treat diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Environmental Sciences
Di Wu, Weixiong Wang, Yanpo Yao, Hongtao Li, Qi Wang, Ben Niu
Summary: Through ecological interactions with various biotic and abiotic agents in soil ecosystems, diverse soil microorganisms establish complex and stable communities in natural settings. These microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling, and play an instrumental role in promoting soil health through bioremediation of pollutants and biocontrol of soil-borne phytopathogens.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Soil Science
Haijing Zhang, Shaojie Wang, Jiaxu Zhang, Chunjie Tian, Shasha Luo
Summary: The study found that biochar application reduced the diversity of soil microbial communities, increased the relative abundance of certain phyla, and decreased others. There were significant differences in the relative abundance of different phyla among different aggregate fractions, and biochar application enhanced microbial interactions in soil, especially in larger aggregates.
SOIL & TILLAGE RESEARCH
(2021)
Review
Microbiology
George Hajishengallis
Summary: Periodontitis and caries are influenced by complex interactions between the oral microbiome and host factors. Animal models have been valuable in understanding the mechanisms of these diseases, although no single model can fully replicate human diseases. This review emphasizes the importance of animal models in proving causality, identifying therapeutic targets, and evaluating novel treatments. Combining animal model-derived findings with in vitro and clinical research can provide a deeper understanding of oral disease pathogenesis.
FEMS MICROBIOLOGY REVIEWS
(2023)
Review
Microbiology
Ju-Hyung Lee, Joo-Hong Park
Summary: The gut microbiome is believed to play a crucial role in metabolic diseases and altering it could lead to metabolic disorders. Manipulating the gut microbiome may represent a new treatment approach for obesity, type 2 diabetes, and nonalcoholic fatty liver disease.
JOURNAL OF MICROBIOLOGY
(2022)
Article
Dentistry, Oral Surgery & Medicine
S. Joseph, M. Carda-Dieguez, J. Aduse-Opoku, A. Alsam, A. Mira, M. A. Curtis
Summary: Periodontal disease leads to changes in cellular profiles and biological activities of both the subgingival microbiome and host tissues. Analysis of a murine periodontal disease model using metatranscriptomics revealed differential expression of 3,468 host transcripts, with 76% being overexpressed in periodontitis. Disease was associated with alterations in immune and inflammatory genes and pathways, as well as cellular/metabolic processes and biological regulation. These metatranscriptome data provide insights into gene expression patterns in periodontal disease and can be used for future functional studies.
JOURNAL OF DENTAL RESEARCH
(2023)
Review
Microbiology
Jens Kreth, Justin Merritt
Summary: The review discusses the use of molecular ecology approaches to study microbiomes. In order to better understand oral diseases, such as caries and periodontitis, it is important to have a deep understanding of the microbial ecological processes that contribute to disease development. This review provides a comprehensive overview of relevant molecular ecology techniques, focusing on oral biofilm development, interspecies interactions, and microbiome biogeography. The described technologies are also applicable to the study of microbiomes from other mucosal sites in the body.
FEMS MICROBIOLOGY REVIEWS
(2023)
Review
Microbiology
Lin Shang, Dongmei Deng, Bastiaan P. Krom, Susan Gibbs
Summary: The oral cavity is a complex and dynamic system where abundant microbes interact with the host and influence oral health. However, the exact mechanisms of host-microbe interactions and their impact on the transition between health and disease are still unclear. Three-dimensional organotypic models of oral tissues have emerged as advanced tools to study these interactions, offering different levels of complexity depending on the research objectives. This review provides an overview of existing 3D oral host-microbe interaction models, comparing their designs, readouts, and discussing their applications and future perspectives.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Norma Torres-Carrillo, Erika Martinez-Lopez, Nora Magdalena Torres-Carrillo, Andres Lopez-Quintero, Jose Miguel Moreno-Ortiz, Anahi Gonzalez-Mercado, Itzae Adonai Gutierrez-Hurtado, Andreas Burkovski
Summary: Microorganisms have a significant impact on human health, including drug therapy. Pharmacomicrobiomics explores how variations in the microbiome affect the disposition, action, and toxicity of drugs. This field is complemented by toxicomicrobiomics and pharmacoecology, which study the influence of the microbiome on drug metabolism and the changes in microbiome caused by drug administration. This review introduces the concept of drug-infection interaction and analyzes the relevance of microorganisms in the host's response to drugs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Qingyi Shao, Danfeng Feng, Zhendi Yu, Danlei Chen, Youqi Ji, Qing Ye, Dongqing Cheng
Summary: This study provides a thorough analysis of the dental plaque microbiome and emphasizes the importance of microbial diversity and interactions in caries progression. The results show that different microorganisms are associated with different stages of caries, and the microbial network becomes more complex as caries progress.
MICROBIAL PATHOGENESIS
(2023)
Article
Biochemistry & Molecular Biology
Kikuye Koyano, Jae Hoon Bahn, Xinshu Xiao
Summary: MicroRNAs (miRNAs) are small non-coding RNAs that play crucial roles in gene regulation. A new bioinformatic method, miNTA, was developed to identify 3' non-templated additions (NTAs) of miRNAs in extracellular biofluids. The study revealed that 3' NTA levels in miRNAs can differentiate between different types of biofluids and these modifications may stabilize base-pairing between miRNAs and their target genes.
Article
Biochemistry & Molecular Biology
Kofi Amoah, Yun-Hua Esther Hsiao, Jae Hoon Bahn, Yiwei Sun, Christina Burghard, Boon Xin Tan, Ei-Wen Yang, Xinshu Xiao
Summary: Alternative splicing is a RNA processing mechanism that affects most genes in human, and can be modulated by genetic variants. Utilizing GTEx data, the study of genetically modulated alternative splicing (GMAS) reveals that GMAS events are shared more frequently across tissues and individuals than expected by chance, indicating a genetically driven nature.
Article
Cell Biology
Feng Li, Fang Wei, Tristan R. Grogan, David E. Elashoff, David Vu, David J. Vigerust, Rohit Gupta, David T. W. Wong
BIOPRESERVATION AND BIOBANKING
(2022)
Article
Oncology
Karolina Elzbieta Kaczor-Urbanowicz, Mustafa Saad, Tristan R. Grogan, Feng Li, You Jeong Heo, David Elashoff, Robert S. Bresalier, David T. W. Wong, Yong Kim
Summary: Gastric cancer is the fourth most common cancer worldwide, mainly affecting the Asian population. Currently, there is no available screening program for gastric cancer in the United States. However, salivary extracellular RNAs show potential as biomarkers for gastric cancer screening. In this study, we validated this method in a U.S. cohort after previously validating it in a Korean cohort.
Article
Multidisciplinary Sciences
Jordan Cheng, Marco Morselli, Wei-Lun Huang, You Jeong Heo, Thalyta Pinheiro-Ferreira, Feng Li, Fang Wei, David Chia, Yong Kim, Hua-Jun He, Kenneth D. Cole, Wu-Chou Su, Matteo Pellegrini, David T. W. Wong
Summary: This study introduces uscfDNA-seq, a single-stranded cell-free DNA sequencing pipeline that reveals a population of ultrashort single-stranded cell-free DNA in human plasma. The ultrashort cell-free DNA is primarily single-stranded and is distributed evenly across chromosomes, with a similar distribution profile over functional elements as the genome, suggesting a possible terminal state of genome degradation.
Article
Microbiology
Jett Liu, Daniel R. Utter, Jie Nie, Kristopher A. Kerns, Eleanor Lamont, Erik L. Hendrickson, Xiaoyan Wang, Jeffrey S. McLean, Xuesong He, Batbileg Bor
Summary: In this study, we report draft genome sequences for nine strains of Candidatus Nanosynbacter sp. HMT-352. These strains and their sequences were used to investigate strain-level variations in host range, gene content, and growth dynamics among the phylum Candidatus Saccharibacteria.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Erik L. Hendrickson, Batbileg Bor, Kristopher A. Kerns, Eleanor Lamont, Yunjie Chang, Jun Liu, Lujia Cen, Fabian Schulte, Markus Hardt, Wenyuan Shi, Xuesong He, Jeffrey S. McLean
Summary: The research reveals that Saccharibacteria Nanosynbacter lyticus establishes a stable epibiotic relationship with its host bacterium, showing dynamic shifts in gene expression and functions during stable symbiosis. These results imply that TM7x and its host bacteria keep a delicate balance to sustain an episymbiotic lifestyle.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Virology
Lujia Cen, Yunjie Chang, Joseph K. Bedree, Yansong Ma, Qiu Zhong, Daniel R. Utter, Pu-Ting Dong, Renate Lux, Batbileg Bor, Jun Liu, Jeffrey S. McLean, Shuai Le, Xuesong He
Summary: Bacteriophages are an important component of the human oral microbiome, with specific phages like LC001 showing remarkable host specificity targeting Schaalia odontolytica. The study suggests that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to access the receptor, facilitating infection.
JOURNAL OF VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Giovanni Quinones-Valdez, Ting Fu, Tracey W. Chan, Xinshu Xiao
Summary: This study introduces an integrative approach called scAllele for detecting single-nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq data. Compared to other commonly used tools, scAllele achieves better performance in identifying nucleotide variants and enables read-specific variant calls and allele-specific splicing analysis.
Article
Oncology
Tracey W. Chan, Jack P. Dodson, Jaron Arbet, Paul C. Boutros, Xinshu Xiao
Summary: RNA editing modifies single nucleotides in RNAs, regulating protein structure and abundance. Dysregulation of RNA editing has been increasingly recognized to play a role in oncology, with large-scale shifts in editing observed in tumors. This study provides the first analysis of RNA editing in single cells from lung cancer, revealing its association with drug resistance and reduced immune response. Furthermore, RNA editing load is a stronger predictor of patient survival than DNA mutations in lung cancer.
Article
Microbiology
Jett Liu, Camden Carmichael, Hatice Hasturk, Wenyuan Shi, Batbileg Bor
Summary: Decades of research have established the importance of oral microbial communities in oral diseases. However, current detection methods are costly and complex. Therefore, a low-cost and rapid detection technique is needed. This study developed a CRISPR-Cas-based assay for the species-specific detection of oral bacteria. The assay showed high specificity and could be easily implemented at point-of-care settings.
JOURNAL OF ORAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Mudra Choudhury, Ting Fu, Kofi Amoah, Hyun-Ik Jun, Tracey W. Chan, Sungwoo Park, David W. Walker, Jae Hoon Bahn, Xinshu Xiao
Summary: This study analyzed RNA editing in postmortem brains of four schizophrenia patient cohorts of European descent and found a significant and consistent trend of hypoediting. A set of schizophrenia-associated editing sites were identified and were found to affect mitochondrial processes. Further experiments showed the functional relevance of two recoding sites in the mitofusin 1 gene to mitochondrial fusion and cellular apoptosis. This study reveals a global reduction of editing in schizophrenia and a strong link between editing and mitochondrial function in the disease.
Article
Medicine, General & Internal
Blake Salfer, Daisy Havo, Skyllar Kuppinger, David T. W. Wong, Feng Li, Liying Zhang
Summary: Liquid biopsy using cell-free DNA (cfDNA) has emerged as a valuable tool for cancer screening and monitoring. While blood-based liquid biopsy has been extensively studied, other body fluids such as saliva offer advantages. Saliva is noninvasive, easily repeatable, and may contain cfDNA from specific types of cancer. However, the lack of standardized pre-analytical procedures for saliva-based testing is a concern. In this study, we assessed pre-analytical variables impacting cfDNA stability in saliva samples. We found that the use of Novosanis's UAS preservative helped stabilize cfDNA in saliva for up to one week at room temperature. Our findings provide valuable insights for the improvement of saliva collection devices and preservation methods.
Article
Biotechnology & Applied Microbiology
Zhiheng Liu, Giovanni Quinones-Valdez, Ting Fu, Elaine Huang, Mudra Choudhury, Fairlie Reese, Ali Mortazavi, Xinshu Xiao
Summary: Although primarily used for characterizing full-length transcripts, long-read RNA-seq can also be utilized to detect nucleotide variants like genetic mutations or RNA editing sites. This study introduces L-GIREMI, a method that effectively handles sequencing errors and read biases, for the detection and analysis of RNA editing sites in long-read RNA-seq data. Results from applying L-GIREMI to PacBio RNA-seq data demonstrate its high accuracy in identifying RNA editing. Furthermore, this analysis provides new insights into the occurrence of RNA editing in single molecules and double-stranded RNA structures. L-GIREMI offers a valuable tool for studying nucleotide variants in long-read RNA-seq.
Article
Microbiology
Jett Liu, Alexander L. Jaffe, Linxing Chen, Batbileg Bor, Jillian F. Banfield
Summary: This study analyzed the CRISPR-Cas systems in Gracilibacteria, Absconditabacteria, and Saccharibacteria, and predicted the phages that infect these bacteria. Some phages were found to infect both standard-coded and alternatively coded CPR bacteria. Additionally, spacers encoded in Actinobacteria were predicted to target some phages of Saccharibacteria.