Article
Biology
Karthik Yarlagadda, Imran Razik, Ripan S. Malhi, Gerald G. Carter
Summary: The study shows evidence of convergence towards a social microbiome among introduced common vampire bats, indicating that social interactions play a significant role in shaping microbiome similarity beyond genetic relatedness, environment, and diet.
Article
Ecology
Mae Berlow, Haruka Wada, Elizabeth P. Derryberry
Summary: The study suggests that noise exposure can increase corticosterone levels and reduce food intake, while also indirectly affecting gut microbial communities through changes in gut microbiome diversity.
Article
Biochemistry & Molecular Biology
Amanda C. Perofsky, Lauren Ancel Meyers, Laura A. Abondano, Anthony Di Fiore, Rebecca J. Lewis
Summary: The study found that permanent social groupings have a significant impact on the gut microbiome composition and dynamics of wild primates, with each social group maintaining unique gut microbial signatures. Individuals with unstable social ties or new immigrants exhibited faster rates of microbiome turnover across seasons.
Article
Biology
Myra C. Hughey, Robin Warne, Alexa Dulmage, Robyn E. Reeve, Grace H. Curtis, Kourtnie Whitfield, Danna M. Schock, Erica Crespi
Summary: This study investigated how increasing salinization and nutritional algae influenced gut bacterial assembly, host physiology, and responses to ranavirus exposure in larval wood frogs. The results showed that elevating salinity and supplementing with algae increased larval growth and ranavirus loads. However, larvae given algae did not exhibit stress responses observed in larvae fed a basic diet, indicating a potentially adaptive stress response reversal. Algal supplementation also reduced gut bacterial diversity, with higher relative abundances of Firmicutes associated with host metabolism and endocrine function regulation.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Medicine, General & Internal
Charissa C. Naidoo, Georgina R. Nyawo, Imran Sulaiman, Benjamin G. Wu, Carolin T. Turner, Kevin Bu, Zaida Palmer, Yonghua Li, Byron W. P. Reeve, Suventha Moodley, Jennifer G. Jackson, Jason Limberis, Andreas H. Diacon, Paul D. van Helden, Jose C. Clemente, Robin M. Warren, Mahdad Noursadeghi, Leopoldo N. Segal, Grant Theron
Summary: This study identified potential microbiome-host interactions in tuberculosis patients and symptomatic controls, showing TB-specific microbial relationships in oral, induced sputum, and stool samples. Cases had specific microbiota characteristics and were associated with host inflammatory pathways.
Article
Microbiology
Bridget N. Chalifour, Diana I. Trifonova, Elizabeth A. Holzhausen, Maximilian J. Bailey, Kelsey A. Schmidt, Mahsa Babaei, Pari Mokhtari, Michael I. Goran, Tanya L. Alderete
Summary: This study evaluated changes in the gut microbiome among Latina mothers who gained or lost weight in the first 6 months after delivery and found significant differences in microbial network density, α- and β-diversity, and relative abundances of bacterial taxa in mothers who gained weight compared to those who lost weight.
Article
Microbiology
Da-Ryung Jung, Hye-Young Yoo, Min-Ji Kim, Vineet Singh, Sung-Ha Park, Minsoo Jeong, Byoung-Jun Park, Jae-Ho Shin
Summary: This study investigated the potential link between skin-gut microorganisms and androgenetic alopecia (AGA) by analyzing the scalp and gut microbiomes of individuals with and without AGA. The findings suggest that the appearance of non-inhabitant bacteria in the scalp increases as hair loss progresses. Bacterial functional differences were also observed in the gut microbiomes of AGA patients, indicating a potential involvement in intestinal homeostasis. Additionally, the networks of the scalp and gut microbiomes were more complex and dense in AGA patients.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Mayank Baranwal, Ryan L. Clark, Jaron Thompson, Zeyu Sun, Alfred O. Hero, Ophelia S. Venturelli
Summary: Researchers have developed a long short-term memory (LSTM) framework to predict and design the functions and dynamics of microbiomes. By analyzing a synthetic human gut community, they found that the LSTM model outperforms traditional ecological models in explaining complex community behaviors. Additionally, they used the LSTM model to uncover microbe-microbe and microbe-metabolite interactions.
News Item
Multidisciplinary Sciences
Jeanne Erdmann
Summary: Faecal transplants have been effective in overcoming resistance to immunotherapies, leading to numerous trials investigating the link between cancer and the microbiome.
Article
Biochemistry & Molecular Biology
Joao S. Rebelo, Celia P. F. Domingues, Francisco Dionisio, Manuel C. Gomes, Ana Botelho, Teresa Nogueira
Summary: Research shows that reducing human contacts leads to a decrease in the diversity of antibiotic resistance genes in human microbiomes. Confinement and hygienic measures not only suppress the spread of pathogenic bacteria in a human network, but also reduce resistance and the need for antibiotic use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Multidisciplinary Sciences
Bianca Nogrady
Summary: Interest in the gut microbiome is creating numerous career and funding opportunities across various fields.
Article
Multidisciplinary Sciences
Ghislaine Cardenas-Posada, Matthew J. Fuxjager
Summary: This study investigates the correlated evolution between head plumage color and drumming behavior in woodpeckers and explores the mechanisms of sexual selection and signal trait combination. The results show a positive correlation between plumage chromatic contrast and drum speed, but no evidence of correlated evolution between drum speed and head color diversity, size of the head's red patch, or extent of the plumage achromatic contrast. Habitat is not a major selective force driving the evolution of head coloration or drumming elaboration.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Xi Zhang, Die Wang, Yafei Zheng, Yingxin Tu, Qingqing Xu, Haowei Jiang, Chen Li, Liangcai Zhao, Yuping Li, Hong Zheng, Hongchang Gao
Summary: The study reveals sexual dimorphism in T1D mice, with female mice showing greater changes in gut microbiota and male mice being more susceptible to T1D in terms of host metabolome. The correlation network analysis suggests that T1D-induced host metabolic changes may be regulated by the gut microbiota in a sex-specific manner, involving SCFAs metabolism, energy metabolism, amino acid metabolism, and choline metabolism.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2021)
Review
Cell Biology
Tzu-Ting Lai, Chia-Wei Liou, Yu-Hsuan Tsai, Yuan-Yuan Lin, Wei-Li Wu
Summary: Psychological stress is a global issue that affects a significant portion of the global population and increases the risk of psychiatric disorders. Recent evidence suggests that the gut microbiota plays a role in regulating stress and associated behavior. The microbiota can modulate stress response through the regulation of intestinal glucocorticoids and the autonomic nervous system. This review provides insight into the pathways by which gut microbes impact stress signaling, brain circuits, and ultimately the host's behavior.
JOURNAL OF BIOMEDICAL SCIENCE
(2023)
Editorial Material
Biochemistry & Molecular Biology
Tomasz Wilmanski, Sean M. Gibbons
Summary: A recent study has shown that the ecological composition of the human gut virome changes with age, with a decline in core taxa and an enrichment of subdominant taxa, similar to what has been observed in the gut bacteriomes of centenarians.
TRENDS IN MICROBIOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Ryan T. Demmer, Angela K. Ulrich, Talia D. Wiggen, Ali Strickland, Brianna M. Naumchik, Shalini Kulasingam, Steven D. Stovitz, Clarisse Marotz, Pedro Belda-Ferre, Greg Humphrey, Peter De Hoff, Louise Laurent, Susan Kline, Rob Knight
Summary: Transmission of SARS-CoV-2 among asymptomatic individuals is possible, leading to concerns about infection in healthcare settings and impacting patient healthcare-seeking behavior. A study screening 489 symptom-free healthcare workers found no positive results for SARS-CoV-2, indicating a prevalence of <1%.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Melissa Y. Chen, Jordan G. Kueneman, Antonio Gonzalez, Greg Humphrey, Rob Knight, Valerie J. McKenzie
Summary: Ecological community traits of host-associated microbiota can predict infection risk and intensity of pathogenic microbes, with richness and proportion being important predictors.
Article
Multidisciplinary Sciences
Brittany D. Needham, Masanori Funabashi, Mark D. Adame, Zhuo Wang, Joseph C. Boktor, Jillian Haney, Wei-Li Wu, Claire Rabut, Mark S. Ladinsky, Son-Jong Hwang, Yumei Guo, Qiyun Zhu, Jessica A. Griffiths, Rob Knight, Pamela J. Bjorkman, Mikhail G. Shapiro, Daniel H. Geschwind, Daniel P. Holschneider, Michael A. Fischbach, Sarkis K. Mazmanian
Summary: The integration of sensory and molecular inputs from the environment has a strong impact on animal behavior. This study focuses on the role of the gastrointestinal tract as a major site of exposure to environmental molecules. The gut microbiota plays a crucial role in behavior, neurotransmitter production, brain development, and myelination patterns in mice. The researchers identified specific genes in the gut microbiome that are responsible for the conversion of dietary tyrosine to a microbial metabolite called 4-ethylphenyl sulfate (4EPS). By engineering gut bacteria, they were able to selectively produce 4EPS in mice. The presence of 4EPS in the brain was associated with changes in activity and functional connectivity in specific brain regions. Furthermore, 4EPS impaired oligodendrocyte maturation in mice, leading to decreased myelination of neuronal axons and anxiety-like behaviors. The behavioral effects of 4EPS were prevented by promoting oligodendrocyte differentiation with pharmacological treatments. This study highlights the influence of a gut-derived molecule on complex behaviors through its effects on oligodendrocyte function and myelin patterning in the brain.
Article
Genetics & Heredity
Youwen Qin, Aki S. Havulinna, Yang Liu, Pekka Jousilahti, Scott C. Ritchie, Alex Tokolyi, Jon G. Sanders, Liisa Valsta, Marta Brozynska, Qiyun Zhu, Anupriya Tripathi, Yoshiki Vazquez-Baeza, Rohit Loomba, Susan Cheng, Mohit Jain, Teemu Niiranen, Leo Lahti, Rob Knight, Veikko Salomaa, Michael Inouye, Guillaume Meric
Summary: A study conducted on a large population-based cohort of 5,959 Finnish individuals identified genetic variations associated with gut microbial abundances. The study found 567 independent SNP-taxon associations, including associations with LCT, ABO, and MED13L genes. The findings shed light on the complex interactions between host genetics and gut microbiota, and their potential role in disease development.
Review
Nutrition & Dietetics
Heather M. Guetterman, Samantha L. Huey, Rob Knight, Allison M. Fox, Saurabh Mehta, Julia L. Finkelstein
Summary: Evidence suggests that vitamin B-12 may be associated with changes in bacterial abundance. While results from in vitro studies suggest that vitamin B-12 may increase alpha-diversity and shift gut microbiome composition (beta-diversity), findings from animal studies and observational human studies were heterogeneous.
ADVANCES IN NUTRITION
(2022)
Article
Microbiology
Robert H. Mills, Parambir S. Dulai, Yoshiki Vazquez-Baeza, Consuelo Sauceda, Noemie Daniel, Romana R. Gerner, Lakshmi E. Batachari, Mario Malfavon, Qiyun Zhu, Kelly Weldon, Greg Humphrey, Marvic Carrillo-Terrazas, Lindsay DeRight Goldasich, MacKenzie Bryant, Manuela Raffatellu, Robert A. Quinn, Andrew T. Gewirtz, Benoit Chassaing, Hiutung Chu, William J. Sandborn, Pieter C. Dorrestein, Rob Knight, David J. Gonzalez
Summary: Multi-omics analysis of faecal samples from patients with ulcerative colitis suggests a connection between Bacteroides vulgatus protease activity and the severity of disease symptoms. Understanding the disruption of host-microbiota interactions in UC is crucial for developing effective treatments. The study demonstrates that the overabundance of B. vulgatus proteases in a subset of UC patients contributes to disease activity. Targeting the protease activity could be a potential strategy for treating UC.
NATURE MICROBIOLOGY
(2022)
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
Microbiology
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vazquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Meric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight
Summary: The operational genomic unit (OGU) method directly exploits sequence alignment hits to individual reference genomes for assessing microbial community diversity and relevance to environmental factors, offering maximal resolution of community composition and supporting phylogenetic methods. The method outperforms taxonomic unit-based analyses in informing biologically relevant insights, as demonstrated in real-world case studies.
Article
Microbiology
George Armstrong, Cameron Martino, Justin Morris, Behnam Khaleghi, Jaeyoung Kang, Jeff DeReus, Qiyun Zhu, Daniel Roush, Daniel McDonald, Antonio Gonazlez, Justin P. Shaffer, Carolina Carpenter, Mehrbod Estaki, Stephen Wandro, Sean Eilert, Ameen Akel, Justin Eno, Ken Curewitz, Austin D. Swafford, Niema Moshiri, Tajana Rosing, Rob Knight
Summary: This study tested the performance of recently developed computational tools Fastp and Minimap2 in metagenomics data preprocessing tasks and compared them with widely used choices Atropos and Bowtie2. The results showed that the new tools achieved faster processing, higher sensitivity, and minimal loss of specificity. Additionally, the taxonomic tables generated from downstream processing provided biologically comparable results. However, the study highlighted that Bowtie2's specificity is still necessary for taxonomic assignment. The authors suggest that regular reevaluation of pipeline components and improvements to standardized APIs can greatly enhance the efficiency of common bioinformatics tasks.
Article
Microbiology
Brandilyn A. Peters, Juan Lin, Qibin Qi, Mykhaylo Usyk, Carmen R. Isasi, Yasmin Mossavar-Rahmani, Carol A. Derby, Nanette Santoro, Krista M. Perreira, Martha L. Daviglus, Michelle A. Kominiarek, Jianwen Cai, Rob Knight, Robert D. Burk, Robert C. Kaplan
Summary: This study explores the relationship between menopause and the gut microbiome in a large Hispanic/Latino population. The findings suggest that postmenopausal women's gut microbiome becomes more similar to that of men, potentially due to the common condition of low estrogen/progesterone levels. Menopause also leads to specific changes in the gut microbiome, including a decrease in certain gut pathogens and a decrease in hormone-related metabolic potential. These changes in the gut microbiome are associated with adverse cardiometabolic risk in postmenopausal women.
Article
Microbiology
Igor Sfiligoi, George Armstrong, Antonio Gonzalez, Daniel McDonald, Rob Knight
Summary: UniFrac is a widely used tool in microbiome research for comparing microbiome profiles. This study adapts UniFrac to be used on graphics processing units, resulting in a significant improvement in computational performance. The tool is successfully applied to the largest 16S rRNA V4 microbiome dataset analyzed to date.
Article
Biotechnology & Applied Microbiology
Clarisse Marotz, Rebecca Molinsky, Cameron Martino, Bruno Bohn, Sumith Roy, Michael Rosenbaum, Moise Desvarieux, Melana Yuzefpolskaya, Bruce J. Paster, David R. Jacobs, Paolo C. Colombo, Panos N. Papapanou, Rob Knight, Ryan T. Demmer
Summary: Periodontitis and diabetes have a high comorbidity rate, which may be partly due to a shared etiology and pathophysiology. This study identified the log-ratio of Treponema to Corynebacterium bacteria as a novel Microbial Indicator of Periodontitis (MIP), which correlates with poor periodontal health and cardiometabolic markers early in disease pathogenesis.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Ecology
James H. Gallagher, David M. Zonana, E. Dale Broder, Aziz M. Syammach, Robin M. Tinghitella
Summary: The emergence of a new mating song in Hawaiian populations of Pacific field cricket, called purring, has been observed. The purring song, produced by heavily modified wing morphology, attracts female crickets and acts as a solution to the conflict between natural and sexual selection. The distribution and characteristics of purring males vary geographically.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2023)
Article
Gastroenterology & Hepatology
Carlos G. Gonzalez, Robert H. Mills, Melissa C. Kordahi, Marvic Carrillo-Terrazas, Henry Secaira-Morocho, Christella E. Widjaja, Matthew S. Tsai, Yash Mittal, Brian A. Yee, Fernando Vargas, Kelly Weldon, Julia M. Gauglitz, Clara Delaroque, Consuelo Sauceda, Leigh-Ana Rossitto, Gail Ackermann, Gregory Humphrey, Austin D. Swafford, Corey A. Siegel, Jay C. Buckey, Laura E. Raffals, Charlotte Sadler, Peter Lindholm, Kathleen M. Fisch, Mark Valaseck, Arief Suriawinata, Gene W. Yeo, Pradipta Ghosh, John T. Chang, Hiutung Chu, Pieter Dorrestein, Qiyun Zhu, Benoit Chassaing, Rob Knight, David J. Gonzalez, Parambir S. Dulai
Summary: This study investigated the molecular mechanisms of hyperbaric oxygen therapy (HBOT) for moderate-to-severe ulcerative colitis. The findings indicate that HBOT reduces neutrophil STAT3 and azurophilic granule activity in UC patients, and improves colitis activity by altering microbial composition and metabolism. The strain-level variations in A muciniphila in the intestinal microbiota may contribute to the nonresponse to HBOT.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Review
Oncology
Jonathan Sholl, Gregory D. Sepich-Poore, Rob Knight, Thomas Pradeu
Summary: This article discusses the unexpected roles of the microbiota in cancer, as well as the microbiota's relevance to cancer development and therapeutic responsiveness. Studying the microbiota can greatly impact clinical oncology research and practice.