Review
Infectious Diseases
Koay Chun Giok, Rohit Kunnath Menon
Summary: It is beneficial to use mechanical debridement augmented with antibiotics for the treatment of peri-implantitis. The microbial profile plays a key role in selecting the appropriate antibiotics. Further studies with standardization and universal clinical parameters are needed for a better understanding of peri-implantitis.
Review
Biochemistry & Molecular Biology
Muhammad Furqan Ashraf, Dan Hou, Quaid Hussain, Muhammad Imran, Jialong Pei, Mohsin Ali, Aamar Shehzad, Muhammad Anwar, Ali Noman, Muhammad Waseem, Xinchun Lin
Summary: Crop production is a major challenge in providing food for the projected 10 billion individuals in 2050. Utilizing genomics and metabolomics strategies can help enhance crop yield and generate stress-tolerant plants. Next-generation sequencing innovation has laid the foundation for understanding genetic potential and improving crops. The application of NGS and metabolomics can improve crop suitability and nutritional value.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Ashley M. Rooney, Amogelang R. Raphenya, Roberto G. Melano, Christine Seah, Noelle R. Yee, Derek R. MacFadden, Andrew G. McArthur, Pierre H. H. Schneeberger, Bryan Coburn
Summary: This study systematically characterized the performance of short-read Illumina sequencing for antimicrobial resistance gene (ARG) detection in metagenomic samples, providing important information for the study design and assessment of human, animal, and environmental metagenomic antimicrobial resistance studies.
Article
Medicine, General & Internal
Eungyung Lee, Suhyun Park, Sunwoo Um, Seunghoon Kim, Jaewoong Lee, Jinho Jang, Hyoung-oh Jeong, Jonghyun Shin, Jihoon Kang, Semin Lee, Taesung Jeong
Summary: This study analyzed the metagenome data of the oral microbiome obtained from Korean children, identified bacteria highly related to dental caries, and studied them with machine learning models. The results showed significant alterations in the oral microbiome according to dental caries and age, which can be used as diagnostic biomarkers.
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Dentistry, Oral Surgery & Medicine
L. H. Heimisdottir, B. M. Lin, H. Cho, A. Orlenko, A. A. Ribeiro, A. Simon-Soro, J. Roach, D. Shungin, J. Ginnis, M. A. Simancas-Pallares, H. D. Spangler, A. G. Ferreira Zandona, J. T. Wright, P. Ramamoorthy, J. H. Moore, H. Koo, D. Wu, K. Divaris
Summary: This study used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence and severity, finding significant associations between various metabolites and ECC. These findings provide novel insights into ECC biology and could serve as the basis for developing measures of disease activity or risk assessment.
JOURNAL OF DENTAL RESEARCH
(2021)
Article
Dentistry, Oral Surgery & Medicine
Bina Yang, Bingqing Song, Jingou Liang, Xuedong Zhou, Biao Ren, Xian Peng, Qi Han, Mingyun Li, Lei Cheng
Summary: Previous studies have shown that there are microorganisms in the oral cavity that promote the occurrence of dental caries, but few studies have been conducted on anticaries materials for these 'core microbiome'. The DMAEM monomer has been found to have an inhibitory effect on the growth of Streptococcus mutans and saliva biofilm, but its effect on the core microbiome of caries needs further research.
Article
Microbiology
Thamirys da Costa Rosa, Aline de Almeida Neves, M. Andrea Azcarate-Peril, Kimon Divaris, Di Wu, Hunyong Cho, Kevin Moss, Bruce J. Paster, Tsute Chen, Liana B. Freitas-Fernandes, Tatiana K. S. Fidalgo, Ricardo Tadeu Lopes, Ana Paula Valente, Roland R. Arnold, Apoena de Aguiar Ribeiro
Summary: This experimental study investigated longitudinal changes in bacterial microbiome and metabolome associated with enamel caries lesion progression and arrest. The results revealed the association of specific microbes and metabolites with caries progression and arrest, providing new insights into the role of biofilm in caries development. These findings offer promising candidate biomarkers for future validation studies.
JOURNAL OF ORAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kyulim Lee, Justin R. Kaspar, Gisela Rojas-Carreno, Alejandro R. Walker, Robert A. Burne
Summary: The study investigated the resistance mechanism of Streptococcus sp. A12 against antimicrobial peptides, with PcfFEG protein playing a key role in combating antimicrobial peptides produced by various isolates of Streptococcus mutans. Deletion of PcfFEG resulted in altered spatial-temporal arrangement between A12 and S. mutans in a dual-species biofilm model.
MOLECULAR MICROBIOLOGY
(2021)
Article
Microbiology
Joao Felipe Besegato, Priscila Borges Gobbo de Melo, Adilson Cesar Abreu Bernardi, Marina Trevelin Souza, Edgar Dutra Zanotto, Vanderlei Salvador Bagnato, Alessandra Nara de Souza Rastelli
Summary: This study evaluates the combined use of experimental ultrasound, aPDT, and bioactive glasses for the removal, decontamination, and remineralization of dentin caries lesions. The results suggest that the combination of ultrasound, aPDT, and bioactive glasses can be a promising minimally invasive treatment for caries lesions.
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Dentistry, Oral Surgery & Medicine
Lais Daniela Ev, Joice Faria Poloni, Naile Dame-Teixeira, Rodrigo Alex Arthur, Daniela Jorge Corralo, Sandra Liana Henz, Thuy Do, Marisa Maltz, Clarissa Cavalcanti Fatturi Parolo
Summary: This study analyzed the functional profile of supragingival biofilm from different enamel caries lesions to understand the diversity of biological processes related to biofilm dysbiosis. The results showed that active and inactive surfaces shared up-regulated genes related to virulence traits, which were not overrepresented in sound surfaces. The study concluded that individual caries status was more important than the surface condition, and suggested pooling samples from different sites, preferably including carious surfaces, in future studies.
JOURNAL OF APPLIED ORAL SCIENCE
(2023)
Article
Dentistry, Oral Surgery & Medicine
Yinuo Wang, Yuwen Zhang, Ting Pan, Huancai Lin, Yan Zhou
Summary: This study investigated the composition and functions discrepancy of supragingival plaque associated with active deciduous teeth caries in mixed dentitions. The results showed no significant differences in microbiome composition between caries and caries-free groups, but metabolome analysis identified glucose metabolism and oxidative stress as related to dental caries in mixed dentitions.
ARCHIVES OF ORAL BIOLOGY
(2022)
Article
Dentistry, Oral Surgery & Medicine
Yinuo Wang, Yuwen Zhang, Ting Pan, Huancai Lin, Yan Zhou
Summary: The study aimed to investigate the composition and functions discrepancy of supragingival plaque associated with active deciduous teeth caries in mixed dentitions. Results showed similar microbiota composition between caries and caries-free groups, but metabolomic analysis revealed biochemical metabolites related to caries status and positively correlated with dominant bacteria.
ARCHIVES OF ORAL BIOLOGY
(2022)
Article
Nutrition & Dietetics
Meng Guo, Jianmin Wu, Weilian Hung, Zhe Sun, Wen Zhao, Hanglian Lan, Zhi Zhao, Guna Wuri, Bing Fang, Liang Zhao, Ming Zhang
Summary: This study found that L. paracasei ET-22 has a significant preventive effect on dental caries in mice. It was also found that ET-22 acts by regulating the microbiota of dental plaques and inhibiting biofilm formation.
Article
Dentistry, Oral Surgery & Medicine
Juliana Philip, Mark J. Buijs, Vincent Y. Pappalardo, Wim Crielaard, Bernd W. Brandt, Egija Zaura
Summary: The study aimed to assess the microbial effects of mechanical debridement in conjunction with a mouthrinse on sites with peri-implant mucositis and gingivitis. The results showed that adjunctive antimicrobial therapy changes the microbial composition, resulting in a less dysbiotic subgingival biofilm in the short term.
JOURNAL OF CLINICAL PERIODONTOLOGY
(2022)
Review
Immunology
Davis R. Zakis, Eva Paulissen, Liga Kornete, A. M. (Marije) Kaan, Elena A. Nicu, Egija Zaura
Summary: The study evaluated the microbial composition of the placenta in healthy pregnancies, showing a low biomass placental microbiota. Some microbial taxa in the placenta may have an oral origin. Most of the included studies had a high risk of quality bias, indicating caution should be used when interpreting the results of individual papers.
JOURNAL OF REPRODUCTIVE IMMUNOLOGY
(2022)
Article
Dentistry, Oral Surgery & Medicine
Amke Marije Kaan, Bernd W. Brandt, Mark J. Buijs, Wim Crielaard, Bart J. F. Keijser, Egija Zaura
Summary: This study compared the microbiota of swabbed and spit saliva. The results showed that there were significant differences in bacterial composition between swabbed and spit saliva, regardless of the operator. Spit saliva had significantly higher Shannon diversity compared to swabbed saliva. Therefore, it is important to collect similar saliva sample types when studying microbial composition.
EUROPEAN JOURNAL OF ORAL SCIENCES
(2022)
Review
Dentistry, Oral Surgery & Medicine
B. T. Rosier, N. Takahashi, E. Zaura, B. P. Krom, R. M. Martinez-Espinosa, S. G. J. van Breda, P. D. Marsh, A. Mira
Summary: This review discusses the association between dietary nitrate and oral health and proposes that microbial nitrate reduction may have benefits for oral health. Nitrate has been shown to increase resilience against salivary acidification, preventing tooth decay. Additionally, nitrate can inhibit sensitive bacteria associated with periodontal diseases. Nitrate may stimulate eubiosis and promote oral health.
JOURNAL OF DENTAL RESEARCH
(2022)
Article
Microbiology
Aurea Simon-Soro, Zhi Ren, Bastiaan P. Krom, Michel A. Hoogenkamp, Pedro J. Cabello-Yeves, Scott G. Daniel, Kyle Bittinger, Inmaculada Tomas, Hyun Koo, Alex Mira
Summary: Microbial aggregates with diverse structures and compositions, including bacteria associated with host cells, are found in human saliva. These aggregates rapidly proliferate and expand during colonization and biofilm initiation, while most single cells remain static or are incorporated by growing aggregates. This alternative biofilm development process involves aggregates adhering to surfaces as growth nuclei and shaping polymicrobial communities at different scales.
Article
Microbiology
Alexa M. G. A. Laheij, Frederik R. Rozema, Michael T. Brennan, Inger von Bultzingslowen, Stephanie J. M. van Leeuwen, Carin Potting, Marie-Charlotte D. N. J. M. Huysmans, Mette D. Hazenberg, Bernd W. Brandt, Egija Zaura, Mark J. Buijs, Johannes J. de Soet, Nicole N. M. Blijlevens, Judith E. Raber-Durlacher
Summary: Stem cell transplantation (SCT) leads to oral microbial dysbiosis, but the oral microbiome recovers after 3 months. Microbial diversity and composition are associated with oral mucositis, but not with oral chronic graft-versus-host disease.
Article
Biochemistry & Molecular Biology
Maria Joao Azevedo, Ricardo Araujo, Joana Campos, Carla Campos, Ana Filipa Ferreira, Ines Falcao-Pires, Carla Ramalho, Egija Zaura, Eugenia Pinto, Benedita Sampaio-Maia
Summary: Yeast transmission from mother to child is an important mechanism in early life, especially through breastfeeding which may transmit antifungal resistant strains. This study isolated and cultured yeast strains from breastmilk, oral, and fecal samples of 73 mother-child pairs, and found 129 isolates from 53% of the pairs, including one antifungal resistant strain transmitted from breastmilk to the child. Most isolates were susceptible to antifungal drugs, but a few resistant strains were also identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Maria Bankvall, Miguel Carda-Dieguez, Alex Mira, Anders Karlsson, Bengt Hasseus, Roger Karlsson, Jairo Robledo-Sierra
Summary: This study investigates the bacterial composition in the oral cavity of patients with oral lichen planus (OLP) and identifies the presence of specific bacterial species associated with OLP, including Streptococcus oralis and Pseudomonas aeruginosa. Metaproteomic analysis reveals the presence of inflammatory and virulence-related proteins in OLP lesions. Further research is needed to determine the role of these bacteria in the development of OLP and their potential as disease biomarkers.
JOURNAL OF ORAL MICROBIOLOGY
(2023)
Article
Microbiology
Alvaro Villanueva-Castellote, Carmen Llena Puy, Miguel Cerda-Dieguez, Alex Mira, Maria D. Ferrer
Summary: The objective of this study was to develop an in vitro model for real-time monitoring of endodontic biofilm growth and evaluate the ex vivo effect of antibiotics on biofilm growth. Biofilm growth was measured through electrical impedance. The bacterial composition of the biofilm was analyzed by Illumina sequencing. The impedance system allowed real-time monitoring of endodontic biofilm formation, and it was proposed as a model for ex vivo evaluation of biofilm susceptibility to antimicrobials.
JOURNAL OF ORAL MICROBIOLOGY
(2023)
Article
Microbiology
Mariana Fernandes, Maria Joao Azevedo, Carla Campos, Ana Filipa Ferreira, Alvaro Azevedo, Ines Falcao-Pires, Egija Zaura, Carla Ramalho, Joana Campos, Benedita Sampaio-Maia
Summary: In early life, maternal factors such as saliva and breastmilk colonization, cardiovascular risk factors, type of delivery, oral health, and caregiving habits play a crucial role in the acquisition of oral microbiome. This study examined the prevalence of potential pathogenic and opportunistic oral bacteria in early life and found a high concordance between mother and child samples, especially in the healthy group. Factors like breastfeeding and mode of delivery were associated with specific types of oral bacteria colonization. This study highlights the importance of maternal factors in the acquisition of oral bacteria and its potential implications for children's health.
Article
Dentistry, Oral Surgery & Medicine
Athina C. C. Georgiou, Suzette V. V. van der Waal, Mark J. J. Buijs, Wim Crielaard, Egija Zaura, Bernd W. W. Brandt
Summary: The aim of this study was to investigate the microbial differences in endodontic infection and their correlation with immunologic markers in blood. A total of 29 teeth with primary or secondary apical periodontitis were analyzed. The microbial profiles were sequenced using Illumina MiSeq, and the inflammatory mediators in blood were examined using mixed models. The results showed that the microbial profiles were associated with endodontic status and presence or absence of pain. Additionally, specific bacteria were correlated with the expression of circulating inflammatory markers.
INTERNATIONAL ENDODONTIC JOURNAL
(2023)
Article
Microbiology
Rodrigo A. Giacaman, Rodrigo Umana, Maria Jose Nunez, Natalia Diaz-Garrido, Constanza Echeverria, Natalia Garcia-Manriquez, Alex Mira, Constanza E. Fernandez, Karla Gambetta-Tessini, Carla P. Lozano
Summary: This study aimed to investigate the impact of saliva dilutions on an in vitro caries model using Streptococcus mutans biofilms. The results showed that even small quantities of saliva could significantly reduce demineralization in enamel and dentin, and the protective effect of saliva was dose-dependent.
Review
Infectious Diseases
Matipaishe Mashayamombe, Miguel Carda-Dieguez, Alex Mira, Robert Fitridge, Peter S. Zilm, Stephen P. Kidd
Summary: The ability of Staphylococcus aureus to colonise different niches across the human body is linked to its adaptable metabolic capability and ability to persist within specific tissues. The relapse of disease in S. aureus infections is due to the presence of suboptimal populations that persist even after the disease is cleared. The constant arousal of these populations is a key strategy for long-term infection and survival of S. aureus.
Article
Biochemistry & Molecular Biology
Natalia Molinero, Diego Taladrid, Irene Zorraquin-Pena, Miguel de Celis, Ignacio Belda, Alex Mira, Begona Bartolome, M. Victoria Moreno-Arribas
Summary: This study compared the differences in the oral microbiome between UC patients and healthy individuals. It found that UC patients have a decrease in alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome. Additionally, specific Staphylococcus members and differential species were only present in UC patients.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Microbiology
Aurea Simon-Soro, Zhi Ren, Bastiaan P. Krom, Michel A. Hoogenkamp, Pedro J. Cabello-Yeves, Scott G. Daniel, Kyle Bittinger, Inmaculada Tomas, Hyun Koo, Alex Mira
Summary: This study investigates the structural organization of microbial aggregates in human saliva and their role in biofilm formation. It reveals that preformed microbial consortia adhere as buds of growth, governing biofilm initiation. These findings provide new insights into spatial and population heterogeneity development in complex ecosystems.