Review
Microbiology
George Hajishengallis, Richard J. Lamont, Hyun Koo
Summary: Oral microbial communities form complex spatial structures and regulate their collective function and adaptability through sophisticated physical and chemical signaling systems. The balance or dysbiosis of these communities, influenced by intra-community interactions, host and environmental factors, plays a crucial role in oral diseases such as periodontitis and dental caries. Dysbiosis in oral polymicrobial communities also has systemic effects, partly due to the colonization of oral pathogens in extra-oral tissues.
CELL HOST & MICROBE
(2023)
Article
Biochemistry & Molecular Biology
Yichen Hu, Amnon Amir, Xiaochang Huang, Yan Li, Shi Huang, Elaine Wolfe, Sophie Weiss, Rob Knight, Zhenjiang Zech Xu
Summary: This study tracked the dynamic changes of the saliva microbiome during human activities through a dense time series data. The results showed that eating activity significantly affected the salivary microbiota composition, with certain bacteria increasing after each meal. The composition of the microbiome also exhibited diurnal oscillation patterns at different taxonomy levels. This research emphasizes the importance of considering daily activities and diurnal factors in the design of oral microbiome studies.
Review
Dentistry, Oral Surgery & Medicine
Valeria Parra-Torres, Samanta Melgar-Rodriguez, Constanza Munoz-Manriquez, Benjamin Sanhueza, Emilio A. Cafferata, Andrea C. Paula-Lima, Jaime Diaz-Zuniga
Summary: Periodontitis is a chronic non-communicable disease caused by a dysbiotic microbiota. Pathogens can spread to the brain, induce an immune response, and lead to the development of Alzheimer's disease (AD). Studies have found oral bacteria in the brains of animals and AD patients, suggesting a potential oral-brain axis in the etiology of AD.
Article
Ecology
Emily B. Graham, Joseph E. Knelman
Summary: Understanding the processes of microbial community assembly is crucial for comprehending the role of microorganisms in ecosystem restoration and for optimizing management strategies. Important factors to consider when evaluating microbial community structure in the context of ecosystem recovery include: variations in community assembly processes, linkages to ecosystem function, and measurable microbial community attributes.
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)
Review
Biochemistry & Molecular Biology
Mireia Mestre, Juan Hofer
Summary: Despite the recent increase in knowledge about microorganisms, the processes determining their global distribution and functioning have not been fully understood. Microbial dormant stages are adapted to specific adverse conditions related to their dispersion path, indicating that dispersion is not completely random. Long-term dormancy enhances microbial dispersion, promoting their ubiquity. The global, recurrent, and spatially cyclical dispersion of microorganisms, known as the Microbial Conveyor Belt, directly influences microbial distribution and the functioning of the Earth system.
TRENDS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Anthony S. Amend, Sean O. I. Swift, John L. Darcy, Mahdi Belcaid, Craig E. Nelson, Joshua Buchanan, Nicolas Cetraro, Kauaoa M. S. Fraiola, Kiana Frank, Kacie Kajihara, Terrance G. McDermot, Margaret McFall-Ngai, Matthew Medeiros, Camilo Mora, Kirsten K. Nakayama, Nhu H. Nguyen, Randi L. Rollins, Peter Sadowski, Wesley Sparagon, Melisandre A. Tefit, Joanne Y. Yew, Danyel Yogi, Nicole A. Hynson
Summary: Microbes are essential for the health, fitness, and metabolism of hosts, and can be found in almost every habitat and organism on Earth. However, we still have limited knowledge about where hosts' microbes reside when they are not on or in the hosts of interest. This study demonstrates that the most species-poor microbiomes are subsets of the most species-rich, and that the microbiomes of plants and animals are nested within those of their environments. Additionally, the distribution of a microbe within a single ecosystem can predict its global distribution, which has implications for understanding global microbial assembly processes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Gordon F. Custer, Luana Bresciani, Francisco Dini-Andreote
Summary: This article discusses the impact of dispersal on the structure and function of microbiomes, as well its importance in ecology and evolution. The authors point out that our understanding of dispersal in microbiomes is relatively limited, but insights can be gained by comparing it to macro-organismal ecology. The article also explores the effects of dispersal on gene influx and allele frequencies, and highlights how successful and unsuccessful dispersal events contribute to the dynamic assembly of microbial communities.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Dentistry, Oral Surgery & Medicine
Nurcan Buduneli
Summary: Periodontal diseases are chronic inflammatory diseases triggered mainly by bacteria and their toxins, with tissue destruction resulting from the host response towards the periodontal microbiome. Environmental factors like tobacco smoking and psychological stress disrupt the symbiotic relationship and affect the balance of the periodontal microbiome.
PERIODONTOLOGY 2000
(2021)
Article
Agriculture, Dairy & Animal Science
Elena G. Olson, Dana K. Dittoe, Joshua A. Jendza, David A. Stock, Steven C. Ricke
Summary: Poultry nutrition and feed manufacturing are crucial for optimizing bird growth and feed conversion by influencing the gastrointestinal microbial composition and functionality. Poultry feeds harbor a characteristic microbial ecosystem consisting of both pathogenic and nonpathogenic microorganisms. However, little is currently known about the nonpathogenic feed microbiome and its impact on the avian gastrointestinal tract.
Review
Microbiology
Reid G. Griggs, Kerri L. Steenwerth, David A. Mills, Dario Cantu, Nicholas A. Bokulich
Summary: Microbiomes play a crucial role in viticulture and winemaking, affecting grape health and wine quality. Understanding the sources and diversity of microbiota in vineyards is important for assessing wine quality and regional characteristics. The microbiota in fruit contributes to wine flavor and aroma, and studying these microbes is essential for evaluating the characteristics of regional wines.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Microbiology
Sonia Nath, Shaju Jacob Pulikkotil, Laura Weyrich, Peter Zilm, Kostas Kapellas, Lisa Jamieson
Summary: This systematic review evaluated the effect of periodontal interventions on the diversity and composition of periodontal microbiota. The results showed that periodontal interventions can decrease bacterial diversity and richness, and alter the composition of oral microbiota.
Article
Dentistry, Oral Surgery & Medicine
M. Arce, M. Rodriguez-Pena, J. Espinoza-Arrue, R. A. Godoy, M. Reyes, T. Kajikawa, T. Greenwell-Wild, G. Hajishengallis, L. Abusleme, N. Moutsopoulos, N. Dutzan
Summary: Periodontitis is a common inflammatory disease characterized by tissue destruction. This study found that cytokines such as IL-6 and IL-23, which are associated with tissue destruction, use a signaling pathway mediated by STAT3. STAT3 activation was found to be increased in epithelial cells and T cells during periodontitis.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Ecology
Dhivya P. Kanisan, Z. B. Randolph Quek, Ren Min Oh, Lutfi Afiq-Rosli, Jen Nie Lee, Danwei Huang, Benjamin J. Wainwright
Summary: Coral-associated bacteria are crucial for maintaining coral health and function. Changes in bacterial community structure due to environmental disturbances can make corals more vulnerable to disease. This study explores the natural variation in coral microbiomes across different regions and host species, and identifies a core microbiome that is shared among all species. These core microbes, such as DMSP metabolizers, play an important role in promoting and maintaining host health. Host identity is a major factor determining microbial community structure, while environmental conditions shape communities at finer scales.
Article
Microbiology
David Danko, Ganesh Babu Malli Mohan, Maria A. Sierra, Michelle Rucker, Nitin K. Singh, Aaron B. Regberg, Mary S. Bell, Niamh B. O'Hara, Rachid Ounit, Christopher E. Mason, Kasthuri Venkateswaran
Summary: NASA conducted a study to evaluate microbial colonization on spacesuits and found a diverse population of microbes, including Bacillus, Arthrobacter, and Ascomycota, present on the surfaces. Results indicate the need for additional measures to prevent microbial contamination of planetary science operations by microbes on the outside of spacesuits.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Jessica A. Grembi, Audrie Lin, Md Abdul Karim, Md Ohedul Islam, Rana Miah, Benjamin F. Arnold, Elizabeth T. Rogawski McQuade, Shahjahan Ali, Md Ziaur Rahman, Zahir Hussain, Abul K. Shoab, Syeda L. Famida, Md Saheen Hossen, Palash Mutsuddi, Mahbubur Rahman, Leanne Unicomb, Rashidul Haque, Mami Taniuchi, Jie Liu, James A. Platts-Mills, Susan P. Holmes, Christine P. Stewart, Jade Benjamin-Chung, John M. Colford Jr, Eric R. Houpt, Stephen P. Luby
Summary: We evaluated the impact of water, sanitation, and handwashing (WSH) and nutrition interventions on enteropathogens in children in Bangladesh. WSH interventions were associated with fewer enteric viruses compared to controls. There was no difference in bacterial and protozoan pathogens for WSH or nutrition interventions.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Statistics & Probability
Claire Donnat, Susan Holmes
Summary: This study examines the evaluation of the reproductive number R for COVID-19 from a Bayesian perspective, explores the impact of heterogeneity on uncertainty quantification, and demonstrates the significant effects of heterogeneity through simulations of transmission and the impact of social distancing strategies.
JOURNAL OF APPLIED STATISTICS
(2023)
Article
Nutrition & Dietetics
Julia Beauchamp-Walters, Gajender Aleti, Lourdes Herrera, Justine Debelius, Natalie Lima, Pritha Dalal, Suzi Hong, Rob Knight, Kyung E. Rhee
Summary: This study aimed to examine the relationship between diet and the gut microbiome in children with medical complexity (CMC) who receive enteral tube feedings, and to determine the impact of different formulas on the CMC microbiome. The results showed that CMC receiving exclusive enteral nutrition had decreased alpha diversity and differences in beta diversity compared with healthy controls, highlighting the importance of diet over medications.
JOURNAL OF PARENTERAL AND ENTERAL NUTRITION
(2023)
Article
Dentistry, Oral Surgery & Medicine
Y. Kurushima, P. M. Wells, R. C. E. Bowyer, N. Zoheir, S. Doran, J. P. Richardson, D. D. Sprockett, D. A. Relman, C. J. Steves, L. Nibali
Summary: Limited evidence is available on how host genetic variants affect microbiota composition. This study examines the associations between candidate host genetic variants and microbial composition in saliva and gut. The findings suggest that certain genetic variants are associated with microbial diversity and composition, and periodontal status may drive variations in the microbiota.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Mathematics, Interdisciplinary Applications
Kris Sankaran, Susan P. Holmes
Summary: By linking conceptual theories with observed data, generative models serve as a crucial tool in various fields such as molecular biology, particle physics, and epidemiology. This article introduces the underlying concepts of generative models and discusses their applications in experimental design, model refinement, goodness-of-fit evaluation, and agent based simulation. The article emphasizes the flexibility of recombining generative mechanisms in different problem contexts and provides practical illustrations and code examples.
ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION
(2023)
Article
Public, Environmental & Occupational Health
Daniel Greene, Megan J. Palmer, David A. Relman
Summary: Scholars and practitioners emphasize the importance of life scientists' proactive role in biosafety and biosecurity. However, existing efforts mainly focus on training technical skills without considering life scientists' motivation. This article argues that promoting proactive biorisk management should pay more attention to life scientists' motivation, and provides examples and strategies for interventions to enhance motivation.
Article
Microbiology
Alexandra D. Switzer, Benjamin J. Callahan, Elizabeth K. Costello, Elisabeth M. Bik, Christine Fontaine, Frances M. D. Gulland, David A. Relman
Summary: Microbial community assembly was studied in harbour seals, showing that the gingival and rectal communities of rehabilitated harbour seals were distinct from formula and pool water, and became increasingly diverse and dissimilar over time, ultimately resembling the communities of local wild harbour seals. Harbour seal microbiota assembly was compared to that of human infants, revealing the rapid emergence of host specificity and evidence of phylosymbiosis, despite being raised by humans. Early life prophylactic antibiotics were associated with changes in the composition of the seal communities and transient increases in alpha diversity, which dissipated over time. These findings highlight the importance of maternal contact and co-housing for neonatal mammals to develop a healthy and resilient microbiota.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Obstetrics & Gynecology
Roberto Romero, Maria Teresa Gervasi, Daniel B. B. DiGiulio, Eunjung Jung, Manaphat Suksai, Jezid Miranda, Kevin R. R. Theis, Francesca Gotsch, David A. A. Relman
Summary: This study aimed to determine whether bacteria, fungi, or archaea are detected in the amniotic fluid of patients who underwent midtrimester amniocentesis for clinical indications. A combination of culture and end-point PCR techniques were used to test amniotic fluid samples from 692 pregnancies. The presence of microorganisms, as determined by culture or a microbial signal in the absence of intra-amniotic inflammation, appears to be a benign condition.
JOURNAL OF PERINATAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Dari Shalon, Rebecca Neal Culver, Jessica A. Grembi, Jacob Folz, Peter V. Treit, Handuo Shi, Florian A. Rosenberger, Les Dethlefsen, Xiandong Meng, Eitan Yaffe, Andres Aranda-Diaz, Philipp E. Geyer, Johannes B. Mueller-Reif, Sean Spencer, Andrew D. Patterson, George Triadafilopoulos, Susan P. Holmes, Matthias Mann, Oliver Fiehn, David A. Relman, Kerwyn Casey Huang
Summary: This study developed an ingestible device that can collect samples from multiple regions of the human intestinal tract during normal digestion. Multi-omics analysis of the collected samples revealed significant differences in bacteria, phages, host proteins, and metabolites between the intestines and stool. The study provides insights into the roles of the gut microbiome and metabolome in human physiology and disease through non-invasive longitudinal profiling of microorganisms, proteins, and bile acids along the intestinal tract.
Article
Biotechnology & Applied Microbiology
Aaron J. Wilk, Alex K. Shalek, Susan Holmes, Catherine A. Blish
Summary: A flexible and scalable framework called Scriabin is presented to analyze cell-cell communication at single-cell resolution. It accurately recovers expected communication edges and uncovers spatial features of interaction. The approach is applicable to various datasets and provides insights into niche-phenotype relationships in health and disease.
NATURE BIOTECHNOLOGY
(2023)
Article
Virology
Kaiming Tao, Soo-Yon Rhee, Philip L. Tzou, Zachary A. Osman, Sergei L. Kosakovsky Pond, Susan P. Holmes, Robert W. Shafer
Summary: In order to manage individuals with detectable viremia and experience with the HIV-1 capsid inhibitor lenacapavir, capsid sequencing is required. By analyzing the published HIV-1 group M capsid sequences, the variability of amino acids at each position and the influence of subtype and cytotoxic T lymphocyte (CTL) selection pressure were characterized.
Article
Multidisciplinary Sciences
Natasha K. Dudek, Jesus G. Galaz-Montoya, Handuo Shi, Megan Mayer, Cristina Danita, Arianna I. Celis, Tobias Viehboeck, Gong-Her Wu, Barry Behr, Silvia Bulgheresi, Kerwyn Casey Huang, Wah Chiu, David A. Relman
Summary: Dudek et al. identified rectangular bacterial structures in the mouths of dolphins. These structures consist of bacterial cells that divide along the longitudinal axis and display unique features. This discovery highlights the need for further exploration of uncultured, host-associated microbes.
NATURE COMMUNICATIONS
(2023)
Article
Endocrinology & Metabolism
Jacob Folz, Rebecca Neal Culver, Juan Montes Morales, Jessica Grembi, George Triadafilopoulos, David A. Relman, Kerwyn Casey Huang, Dari Shalon, Oliver Fiehn
Summary: This study used a non-invasive, ingestible sampling device to collect and analyze intestinal samples and stool samples from 15 healthy participants. The research found significant differences in food metabolites between stool and intestines, and the intestinal metabolome can reflect the connection between diet, host, and microbial metabolism.
Article
Multidisciplinary Sciences
Elizabeth K. K. Costello, Daniel B. B. DiGiulio, Anna Robaczewska, Laura Symul, Ronald J. J. Wong, Gary M. M. Shaw, David K. K. Stevenson, Susan P. P. Holmes, Douglas S. S. Kwon, David A. A. Relman
Summary: Childbirth leads to vaginal inflammation and a decrease in Lactobacillus dominance, which continues to affect women for up to one year postpartum. Only 49.4% of women were able to recover from this disturbance by the end of the first postpartum year, indicating a significant impact on women's health and future pregnancies.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Arianna I. Celis, David A. Relman, Kerwyn Casey Huang
Summary: This article focuses on the responses of the gut microbiota to iron supplementation in humans. The study finds that iron can cause gradual changes in the composition of the microbiota, and deprivation of iron leads to growth inhibition and reduction in diversity. Individual species' sensitivity to iron deprivation can predict their dependency in a community. Exogenous heme serves as a source of inorganic iron to prevent depletion of certain species. The results highlight the importance of combining in vivo and in vitro studies in understanding the impact of environmental factors on the gut microbiota.
CELL CHEMICAL BIOLOGY
(2023)
