Article
Microbiology
Arthur Monjot, Gisele Bronner, Damien Courtine, Corinne Cruaud, Corinne Da Silva, Jean-Marc Aury, Frederick Gavory, Anne Mone, Agnes Vellet, Ivan Wawrzyniak, Jonathan Colombet, Hermine Billard, Didier Debroas, Cecile Lepere
Summary: The advent of high-throughput sequencing has revealed the diverse microbial eukaryotes in aquatic ecosystems, but their function and contribution to the trophic food web in freshwater ecosystems are not well understood. This study used a morpho-physio-phenological traits-based approach to infer functional groups of microbial eukaryotes and analysed metatranscriptomic data to assess their metabolic potential. The analysis showed a high diversity of microbial eukaryotes in the deep water layer, with saprotrophs expressing transcripts related to sulfur and nitrate metabolism, as well as organic matter degradation. Seasonal variations were observed in the mixolimnion, particularly for parasites and mixoplankton. Water mixing during spring and autumn promoted the dissemination of parasitic fungi and over-expression of genes involved in the parasitic cycle. Mixoplanktonic haptophytes showed an advantage in phagotrophy under nutrient limitation.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jaclyn K. Saunders, Matthew R. McIlvin, Chris L. Dupont, Drishti Kaul, Dawn M. Moran, Tristan Horner, Sarah M. Laperriere, Eric A. Webb, Tanja Bosak, Alyson E. Santoro, Mak A. Saito
Summary: Enzymes play a crucial role in Earth's life-sustaining biogeochemical cycles. In this study, metaproteomics was used to investigate the enzymatic capabilities of microbial communities in the central Pacific Ocean. The results showed abundant key functions as well as diverse functions, with the microbial community being influenced by environmental features and displaying variations at different scales. The study also identified previously understudied metabolic pathways and provided important empirical data for biogeochemical models.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Felix M. Kibegwa, Rawlynce C. Bett, Charles K. Gachuiri, Eunice Machuka, Francesca Stomeo, Fidalis D. Mujibi
Summary: The objective of this study was to investigate the effect of varying roughage and concentrate proportions on the composition and functional genes of rumen and fecal microbiota in crossbreed dairy cattle. Results showed that dietary modifications significantly affected the microbial composition in the rumen, with an increase in concentrate leading to an upsurge in Proteobacteria and a reduction in Bacteroidetes and Firmicutes. However, changes in microbial composition in fecal samples were inconsistent with dietary modifications. Carbohydrate and protein metabolism pathways dominated microbial roles, and a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a reduction in protein synthesis. Moreover, microbial stress-related responses were identified, with Bacteroides and Clostridium genera as the principal hosts.
Article
Multidisciplinary Sciences
William R. Shoemaker, Stuart E. Jones, Mario E. Muscarella, Megan G. Behringer, Brent K. Lehmkuhl, Jay T. Lennon
Summary: Research shows that under limited resources, most bacterial taxa can survive, with a wide range of extinction times. Despite the lack of exogenous resources, bacterial populations continue to evolve and acquire numerous mutations. While adapting to environmental pressures, bacterial lifespan is extended through scavenging dead cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Agriculture, Dairy & Animal Science
Antonio M. Silvestre, Ana Carolina J. Pinto, Werner F. Schleifer, Lidiane S. Miranda, Leandro A. F. Silva, Daniel M. Casali, Katia L. R. Souza, Vanessa G. L. Gasparini, Gustavo D. Cruz, Garret Suen, Danilo D. Millen
Summary: This study examined the relationship between rumen microbial community, rumen morphometrics, feeding behavior, feedlot performance, and carcass characteristics of Nellore cattle classified by residual feed intake (RFI). The results showed that the ruminal microbial community was not affected by different levels of RFI, suggesting that the differences in feed efficiency of Nellore cattle are associated with other factors.
Article
Multidisciplinary Sciences
Alexa M. Nicolas, Ella T. Sieradzki, Jennifer Pett-Ridge, Jillian F. Banfield, Michiko E. Taga, Mary K. Firestone, Steven J. Blazewicz
Summary: This study investigates the response of viruses and microbes in soil to wet-up. The results show that wet-up leads to a decrease in viral richness but an increase in viral biomass, and viral lysis plays an important role in microbial death following wet-up.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Carolina Gutierrez-Chavez, Nicole Benaud, Belinda C. Ferrari
Summary: Lipopeptides (LPs) are secondary metabolites produced by various bacteria and fungi, with important biotechnological applications in emulsification, antitumor, immunomodulatory, and antimicrobial activities. Despite limited understanding of the ecological role of LPs, research on their mode of action in biofilm formation, antimicrobial activity, etc., can provide insights into their roles in the natural environment.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Thea Os Andersen, Benoit J. Kunath, Live H. Hagen, Magnus O. Arntzen, Phillip B. Pope
Summary: The rumen microbiome is a complex mixture of anaerobic bacteria, archaea, protozoa, viruses, and fungi that interact closely to degrade and ferment plant material into nutrients for host metabolism, producing methane gas as a by-product. Understanding the rumen microbiome is important for animal health, nutrition, and global greenhouse gas emissions. Advances in meta-omic techniques, such as metaproteomics, enable exploration into active microbial populations in the rumen and accurate reconstruction of their metabolic functions.
Article
Veterinary Sciences
Kampanat Phesatcha, Burarat Phesatcha, Krittika Chunwijitra, Metha Wanapat, Anusorn Cherdthong
Summary: The addition of dry yeast (DY) to fattening steers with a high concentrate diet improved feed intake, nutrient digestibility, rumen ecology, and growth performance, while mitigating ruminal methane production.
VETERINARY SCIENCES
(2021)
Article
Veterinary Sciences
Juan Manuel Palma-Hidalgo, David R. Yanez-Ruiz, Elisabeth Jimenez, A. Ignacio Martin-Garcia, Alejandro Belanche
Summary: The study found that rearing newborn goat kids in contact with adult companions promoted rumen microbial development, leading to better physiological development prior to weaning.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Ecology
Arthur Escalas, Fabiana S. Paula, Francois Guilhaumon, Mengting Yuan, Yunfeng Yang, Linwei Wu, Feifei Liu, Jiaje Feng, Yuguang Zhang, Jizhong Zhou
Summary: The study used macroecological models to examine the distribution of microbial functional genes in soil systems, revealing different characteristics and distribution patterns of genes.
Review
Microbiology
Peter Rubbens, Ruben Props
Summary: Flow cytometry is crucial for studying microbial communities, allowing for rapid generation of quantitative, multivariate single-cell data with high temporal resolution. A streamlined data processing workflow is necessary due to the complexity and amount of data, with a lack of comprehensive overview on the computational analysis steps currently. This review provides an overview of the data analysis pipeline tailored to microbial ecology studies, highlighting potentially useful computational methods and addressing open challenges in the field.
Article
Ecology
Zongjun Li, Xiangnan Wang, Yu Zhang, Zhongtang Yu, Tingting Zhang, Xuelei Dai, Xiangyu Pan, Ruoxi Jing, Yueyang Yan, Yangfan Liu, Shan Gao, Fei Li, Youqin Huang, Jian Tian, Junhu Yao, XvPeng Xing, Tao Shi, Jifeng Ning, Bin Yao, Huoqing Huang, Yu Jiang
Summary: Understanding the biodiversity and genetics of gut microbiomes is important for host physiology and industrial enzymes. In this study, high-quality ciliate genomes were acquired using single-cell sequencing, providing insights into the taxonomy, phylogeny, and carbohydrate degradation capabilities of rumen ciliates. The ciliate dataset also facilitated metagenomic analysis of rumen microbiota.
Article
Multidisciplinary Sciences
Raphael Morard, Christiane Hassenruck, Mattia Greco, Antonio Fernandez-Guerra, Sylvain Rigaud, Christophe J. Douady, Michal Kucera
Summary: Planktonic foraminifera are important for understanding ancient climate and the evolution of plankton. The origins of these organisms are unclear, but a molecular clock suggests that benthic foraminifera dispersed in the plankton and renewed the diversity of planktonic foraminifera after a mass extinction event. This study shows that calcareous benthic foraminifera are able to actively disperse in the plankton and that modern planktonic clades originated from different benthic ancestors. These findings challenge the classical interpretation of the fossil record and suggest that the diversity of planktonic foraminifera is continuously fueled by benthic foraminifera.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Claire A. Shaw, Yuna Park, Maria Gonzalez, Rich A. Duong, Pramod K. Pandey, Charles G. Brooke, Matthias Hess
Summary: Researchers evaluated three different artificial rumen systems and found that all systems were capable of maintaining stable pH, redox potential, and temperature. The semi-continuous ARS was more accurate in simulating the rumen microbiome.
FERMENTATION-BASEL
(2023)
Article
Gastroenterology & Hepatology
Erin R. Shanahan, Seungha Kang, Heidi Staudacher, Ayesha Shah, Anh Do, Grace Burns, Veronique S. Chachay, Natasha A. Koloski, Simon Keely, Marjorie M. Walker, Nicholas J. Talley, Mark Morrison, Gerald J. Holtmann
Summary: This study indicates a link between duodenal microbiota, gastric emptying, and FD symptoms, and this link is largely independent of long-term dietary intake.
Article
Gastroenterology & Hepatology
Ayesha Shah, Seungha Kang, Nicholas J. Talley, Anh Do, Marjorie M. Walker, Erin R. Shanahan, Natasha A. Koloski, Michael P. Jones, Simon Keely, Mark Morrison, Gerald J. Holtmann
Summary: Patients with functional gastrointestinal disorders (FGIDs) often report intolerance to wheat products. This study compared various factors, including gastrointestinal symptoms, sensory function, psychiatric comorbidities, gut-homing immune cells, and duodenal mucosa-associated microbiome (d-MAM), between FGID patients and controls with and without self-reported wheat sensitivity (SR-NCWS). The results showed that anxiety, visceral sensory function, and specific bacterial taxa were associated with FGID, while gut-homing T-cells were associated with SR-NCWS. The study also found differences in the bacterial genera between the FGID subtypes and controls. Patients with FGID, with or without SR-NCWS, showed increased symptom response and anxiety scores compared to controls.
Article
Green & Sustainable Science & Technology
Alejandro Belanche, Alexander N. Hristov, Henk J. van Lingen, Stuart E. Denman, Ermias Kebreab, Angela Schwarm, Michael Kreuzer, Mutian Niu, Maguy Eugene, Vincent Niderkorn, Cecile Martin, Harry Archimede, Mark McGee, Christopher K. Reynolds, Les A. Crompton, Ali Reza Bayat, Zhongtang Yu, Andre Bannink, Jan Dijkstra, Alex Chaves, Harry Clark, Stefan Muetzel, Vibeke Lind, Jon M. Moorby, John A. Rooke, Aurelie Aubry, Walter Antezana, Min Wang, Roger Hegarty, V Hutton Oddy, Julian Hill, Philip E. Vercoe, Jean Victor Savian, Adibe Luiz Abdalla, Yosra A. Soltan, Alda Lucia Gomes Monteiro, Juan Carlos Ku-Vera, Gustavo Jaurena, Carlos A. Gomez-Bravo, Olga L. Mayorga, Guilhermo F. S. Congio, David R. Yanez-Ruiz
Summary: This study developed empirical models to predict enteric methane emissions from sheep using a global database. The models showed that including variables such as body weight and organic matter digestibility improved prediction accuracy. Age-specific equations were also found to enhance prediction performance. The study concluded that predicting sheep methane production requires considering variables such as dry matter intake, body weight, and rumen propionate proportion, and appropriate universal equations can be used across different diets and climatic conditions.
JOURNAL OF CLEANER PRODUCTION
(2023)
Review
Neurosciences
Alexander N. Boytar, Marloes Dekker Nitert, Mark Morrision, Tina L. Skinner, David G. Jenkins
Summary: Physical activity is associated with reduced risks of colorectal cancer incidence, recurrence and mortality. The mechanism/s underlying this association remain unclear, but growing evidence suggests that different characteristics of the gut microbiota may play a role. Exercise can modify the gut microbiota, promoting its anti-tumorigenic characteristics, but further research is needed in the context of colorectal cancer.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Medicine, Research & Experimental
Samuel Chan, Carmel M. M. Hawley, Elaine M. M. Pascoe, Christopher Cao, Katrina L. L. Campbell, Scott B. B. Campbell, Ross S. S. Francis, Rachael Hale, Nicole M. M. Isbel, Mark Morrison, David W. W. Johnson
Summary: This study aims to assess the feasibility of prebiotic supplementation in reducing infections and gastrointestinal symptoms in kidney transplant recipients. Sixty recipients will be recruited for a double-blind, placebo-controlled, randomised trial to receive prebiotic therapy or placebo for 4-6 weeks. The outcomes will include recruitment, adherence, tolerance, laboratory parameters, quality of life, gastrointestinal symptoms, and clinical outcomes.
PILOT AND FEASIBILITY STUDIES
(2023)
Article
Immunology
Md. Al Amin Sikder, Ridwan B. Rashid, Tufael Ahmed, Ismail Sebina, Daniel R. Howard, Md. Ashik Ullah, Muhammed Mahfuzur Rahman, Jason P. Lynch, Bodie Curren, Rhiannon B. Werder, Jennifer Simpson, Alec Bissell, Mark Morrison, Carina Walpole, Kristen J. Radford, Vinod Kumar, Trent M. Woodruff, Tan Hui Ying, Ayesha Ali, Gerard E. Kaiko, John W. Upham, Robert D. Hoelzle, Paraic O. Cuiv, Patrick G. Holt, Paul G. Dennis, Simon Phipps
Summary: Poor maternal diet during pregnancy increases the risk of severe lower respiratory infections (sLRIs) in infants. This study found that a maternal low-fiber diet (LFD) led to worsened LRI severity in mice offspring due to delayed recruitment of plasmacytoid dendritic cells (pDC) and disruption of regulatory T cell expansion in the lungs. The LFD altered the composition of the maternal milk and infant gut microbiome, resulting in reduced secretion of the DC growth factor Flt3L and impaired pDC hematopoiesis. However, therapy with propionate-producing bacteria or propionate supplementation restored gut Flt3L expression and pDC hematopoiesis, providing protection against sLRI.
Review
Gastroenterology & Hepatology
Ayesha Shah, Veenaa Pakeerathan, Michael P. Jones, Purna C. Kashyap, Kate Virgo, Thomas Fairlie, Mark Morrison, Uday C. Ghoshal, Gerald J. Holtmann
Summary: This systematic review and meta-analysis investigated the prevalence of small intestinal bacterial overgrowth (SIBO) in systemic sclerosis (SSc), as well as the risk factors and the effects on gastrointestinal symptoms. The study found that SIBO prevalence in SSc patients is 39.9%, with a 10-fold increased prevalence compared to controls. It also suggested that antimicrobial therapy should be considered for SSc patients with SIBO and diarrhea.
JOURNAL OF NEUROGASTROENTEROLOGY AND MOTILITY
(2023)
Article
Gastroenterology & Hepatology
J. J. Jimenez Loayza, S. Kang, L. Schooth, J. J. Teh, A. de Klerk, E. K. Noon, J. Zhang, J. Hu, A. L. Hamilton, A. Wilson-O'Brien, G. L. Trakman, W. Lin, J. Ching, L. Or, J. J. Y. Sung, J. Yu, S. C. Ng, M. A. Kamm, M. Morrison
Summary: Food additives have been found to affect the microbial dysbiosis associated with Crohn's disease. Sodium sulfite and polysorbate 80 have inhibitory effects on beneficial bacteria, while polysorbate 80 and carboxymethylcellulose can drive changes in the CD mucosa-associated microbiota, leading to early disease recurrence.
Article
Multidisciplinary Sciences
Gonzalo Cantalapiedra-Hijar, Gonzalo Martinez-Fernandez, Evelyne Forano, Stuart E. Denman, Diego Morgavi, Christopher S. Mcsweeney
Summary: This study investigates the impact of rumen bacteria on nitrogen isotopic discrimination and confirms their key role in Δ15Nanimal-diet.
Meeting Abstract
Gastroenterology & Hepatology
Lauren F. Schooth, Ahmed Sid Ahmed, Seungha Kang, Ayesha Shah, Thomas Fairlie, Jing Jie Teh, Yenkai Lim, Emily C. Hoedt, Nicholas J. Talley, Simon Keely, Gerald J. Holtmann, Mark Morrison
Meeting Abstract
Gastroenterology & Hepatology
Ayesha Shah, Peter R. Sternes, Camila Ayala Pintos, Seungha Kang, Michael P. Jones, Gene Tyson, Mark Morrison, Gerald J. Holtmann
Meeting Abstract
Gastroenterology & Hepatology
Sonja Drljaca, Valeria Vollenbroich, Jing Jie Teh, Seungha Kang, Jingwan Zhang, Jielun Hu, Amy L. Hamilton, Amy Wilson-O'Brien, Jessica Y. Ching, Winnie Y. Lin, Gina L. Trakman, Joseph Sung, Jun Yu, Siew C. Ng, Michael A. Kamm, Mark Morrison
Article
Rheumatology
P. R. Sternes, L. Brett, J. Phipps, F. Ciccia, T. Kenna, E. de Guzman, K. Zimmermann, M. Morrison, G. Holtmann, E. Klingberg, D. Mauro, C. McIvor, H. Forsblad-d'Elia, M. A. Brown
Summary: The gut microbiomes of AS and AS-IBD patients are different from IBD patients and healthy controls, indicating a distinct role of the gut in driving AS compared with IBD. However, the presence of potentially pathogenic genera shared between both diseases suggests a common microbial trigger of disease.
ARTHRITIS RESEARCH & THERAPY
(2022)
