Article
Environmental Sciences
Kejin Chen, Rong He, Li'ao Wang, Lingyue Liu, Xin Huang, Juan Ping, Chuan Huang, Xiang Wang, Yuanyuan Liu
Summary: In shale gas mining areas, indigenous microorganisms can degrade organic pollutants such as petroleum hydrocarbons into CO2 and H2O through aerobic metabolism, but a large quantity of CO2 emissions can exacerbate the greenhouse effect. The experiment found that the removal rate of petroleum hydrocarbons was significantly lower under high-concentration pollution compared to low and medium concentrations, with the largest removal rate in the early stage of culture for each group's TPH concentration. Additionally, the main carbon fixation pathway identified in the study was the reductive citric acid cycle.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Hiroto Miura, Masayuki Takeda, Megumi Yamaguchi, Yoshihisa Ohtani, Go Endo, Yasuhisa Masuda, Kaede Ito, Yoshio Nagura, Kunihiro Iwashita, Tomohiro Mitani, Yutaka Suzuki, Yasuo Kobayashi, Satoshi Koike
Summary: This study established a high-resolution and high-throughput rumen microbial profiling approach by combining the MinION platform and buccal swab samples, which could potentially be applied in large-scale studies for rumen microbial analysis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Xuan Liu, Zhenhua Ma, Yanfei Wang, Li Li, Hao Jia, Lihuan Zhang
Summary: Probiotics, especially compound probiotics, showed positive effects on broiler growth performance, carcass characteristics, intestinal barrier, and early gut immune-related genes. The 16S rDNA amplicon sequencing analysis revealed an increase in beneficial microbes and a decrease in harmful microbes in the cecum's gut microbiota of 42-day-old broilers under probiotic treatment. Functional analysis indicated enrichment in DNA replication, transcription, and glycolysis processes in probiotic-treated broilers.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Environmental Sciences
Fang-Zhou Gao, Liang-Ying He, Li-Xin Hu, Jun Chen, Yuan-Yuan Yang, Hai-Yan Zou, Lu-Xi He, Hong Bai, You-Sheng Liu, Jian-Liang Zhao, Guang-Guo Ying
Summary: This study found that bacterial communities in river water and sediment are influenced differently by seasonal variations and anthropogenic activities, with the water bacterial communities also impacted by emerging pollutants. The dominant phyla Proteobacteria and Firmicutes showed adaptability to various affected regions, with associations to antibiotic resistance. Levels of antibiotics, antibiotic resistance genes, and non-antibiotic pharmaceuticals were closely related to bacterial community composition and diversity, indicating their role in shifting bacterial communities.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Wenke Zhang, Xiaoquan Fan, Haobo Shi, Jian Li, Mingqian Zhang, Jin Zhao, Xiaoquan Su
Summary: In this study, a comprehensive method called Qscore was proposed to evaluate the performance of 16S rRNA amplicons in microbial profiling. The method integrated factors such as amplification rate, taxonomic annotation, sequence type, and length. Evaluation of a wide range of microbe species and microbiomes showed that the Qscore-suggested parameters resulted in high precision in microbiome profiling. This study has significant implications for guiding future microbiome studies and enabling the reuse of massive sequence data.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agriculture, Dairy & Animal Science
Y. K. Zhang, X. X. Zhang, F. D. Li, C. Li, G. Z. Li, D. Y. Zhang, Q. Z. Song, X. L. Li, Y. Zhao, W. M. Wang
Summary: The rumen microbiota in sheep is associated with residual feed intake (RFI), with low-RFI sheep exhibiting a more abundant and diverse microbiome.
Article
Microbiology
Kayla M. Williamson, Brandie D. Wagner, Charles E. Robertson, Mark J. Stevens, Marci K. Sontag, Peter M. Mourani, J. Kirk Harris
Summary: The study aimed to increase the sensitivity of bacterial community analysis without impacting community composition or interfering with cluster formation during sequencing. The modified PCR protocol showed increased sensitivity in detecting bacterial communities in airway samples, crucial for studying the highly variable human airway microbiome.
Article
Nutrition & Dietetics
Yanzhou Hu, Jia Xu, Yao Sheng, Junyu Liu, Haoyu Li, Mingzhang Guo, Wentao Xu, Yunbo Luo, Kunlun Huang, Xiaoyun He
Summary: The study revealed that Pleurotus ostreatus can prevent obesity, maintain glucose homeostasis, and beneficially modulate gut microbiota. It modified the composition and functions of gut microbiota in obese mice and made them similar to those in lean mice, contributing to weight loss.
Article
Microbiology
Indira J. Quintero, Anakena M. Castillo, Luis C. Mejia
Summary: This study compared the bacterial communities in soil of two mangrove forest sites in the Panama Bay and found that the community was more diverse in the rural mangrove forest. The dominant phyla of bacteria shared between the two sites were Proteobacteria, Desulfobacterota, and Chloroflexi. The relative abundance of certain bacterial genera increased in the transition from dry to rainy season in the urban mangrove forest.
Article
Veterinary Sciences
Yang Yu, Xin Li, Ziyao Liu, Ying Xu, Yue Shen, Guoji Li, Xianhui Huang
Summary: The newly developed chlortetracycline rumen-protected granules are relatively harmless to rumen microorganisms while effectively treating lamb E.coli diarrhea. The study showed that the granules could diminish the impact of chlortetracycline on rumen microorganisms compared with the premix. The oral administration of the chlortetracycline rumen-protected granules effectively treated lamb diarrhea caused by E.coli.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Ezgi Ozkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram, Falk Hildebrand
Summary: LotuS2 is a lightweight and user-friendly pipeline for amplicon sequence analysis, offering high speed and precision, as well as improved data quality through extensive pre- and post-processing steps.
Article
Immunology
Vitor Heidrich, Lilian T. Inoue, Paula F. Asprino, Fabiana Bettoni, Antonio C. H. Mariotti, Diogo A. Bastos, Denis L. F. Jardim, Marco A. Arap, Anamaria A. Camargo
Summary: Accessibility to next-generation sequencing (NGS) has enabled the profiling of microbial communities. Choosing the right 16S rRNA hypervariable region for sequencing is critical. This study evaluated the performance of different hypervariable regions in male urinary microbiota profiling and found that V1V2 region is more suitable.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Ecology
Julio Cesar Garcia-Sanchez, Jose Arredondo-Centeno, Maria Guadalupe Segovia-Ramirez, Ariadna Marcela Tenorio Olvera, Gabriela Parra-Olea, Vance T. Vredenburg, Sean M. Rovito
Summary: Factors such as host phylogeny and climate influence the composition of microbial communities on amphibian skin. The composition of bacterial communities is correlated with host phylogeny, while fungal communities are associated with temperature seasonality and precipitation. Co-occurrence networks of bacteria and fungi show differences in connectivity and negative associations. Including fungi in future studies can provide insights into functional interactions within the microbiome.
Article
Agricultural Engineering
Marco Wehner, Irene Kleidorfer, Ingrid Whittle, Daniela Bischof, Anke Bockreis, Heribert Insam, Wolfgang Mueller, Sebastian Hupfauf
Summary: Enormous amounts of food waste are produced worldwide, and proper disposal strategies are needed. Anaerobic digestion to produce biomethane is a promising strategy, but storage and delivery solutions are required. This study assessed a decentralized system for demand-oriented food waste storage and found that it can be stored without cooling, as lactic acid produced by bacteria stabilizes the material and inactivates pathogens. The storage had no negative impact on methane yield and contained readily degradable substances for biogas production.
BIORESOURCE TECHNOLOGY
(2023)
Article
Environmental Sciences
Kusum Dhakar, Shlomit Medina, Hamam Ziadna, Karam Igbaria, Guy Achdari, Ran Lati, Raphy Zarecki, Zeev Ronen, Guy Dovrat, Hanan Eizenberg, Shiri Freilich
Summary: Microbial communities in different crop fields respond differently to the application of the herbicide atrazine, as revealed by 16S rRNA gene amplicon sequencing. The nutrient-poor soil showed a different response compared to the nutrient-rich soils, both in terms of atrazine persistence and its effect on bacterial community structure and composition. Specific bacterial degraders of atrazine were more abundant in the contaminated nutrient-poor soil, while bacteria involved in nitrogen cycling were more abundant in the contaminated nutrient-rich soil. Understanding these responses can help in designing precision application strategies.
ENVIRONMENTAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Elizabeth H. Hart, Sarah R. Christofides, Teri E. Davies, Pauline Rees Stevens, Christopher J. Creevey, Carsten T. Mueller, Hilary J. Rogers, Alison H. Kingston-Smith
Summary: This study investigated how the plant response to climate change affects forage quality and subsequent rumen fermentation. The results indicate that breeding future forage varieties should target tolerance of acute stress rather than long term climate.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Isabela Maria Fernandes de Oliveira, Fernanda Godoy-Santos, Linda Boniface Oyama, Sofia Magalhaes Moreira, Rodrigo Goncalves Dias, Sharon Ann Huws, Christopher J. Creevey, Hilario Cuquetto Mantovani
Summary: This study characterized the genetic features of Streptococcus lutetiensis through whole-genome sequencing, revealing its antimicrobial activity and adaptation to the rumen environment. The genome of S. lutetiensis UFV80 contained a putative CRISPR-Cas9 system, while all bacterial genomes harbored genetic clusters related to the biosynthesis of bacteriocins. SDS-PAGE confirmed the predicted class II bacteriocins. These findings highlight the importance of this research.
Article
Microbiology
Katie Lawther, Fernanda Godoy Santos, Linda Boniface Oyama, Francesco Rubino, Steven Morrison, Chris J. Creevey, John W. McGrath, Sharon Ann Huws
Summary: This study reveals the diverse and abundant antimicrobial resistance gene reservoirs present in both livestock and soil microbiomes, highlighting the significant risks to human and animal health. The analysis of a large number of samples from various countries provides a global insight into resistomes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Linda B. Oyama, Hamza Olleik, Ana Carolina Nery Teixeira, Matheus M. Guidini, James A. Pickup, Brandon Yeo Pei Hui, Nicolas Vidal, Alan R. Cookson, Hannah Vallin, Toby Wilkinson, Denise M. S. Bazzolli, Jennifer Richards, Mandy Wootton, Ralf Mikut, Kai Hilpert, Marc Maresca, Josette Perrier, Matthias Hess, Hilario C. Mantovani, Narcis Fernandez-Fuentes, Christopher J. Creevey, Sharon A. Huws
Summary: This study identified two antimicrobial peptides, HG2 and HG4, from a rumen microbiome metagenomic dataset. These peptides showed activity against methicillin-resistant Staphylococcus aureus (MRSA) strains, including anti-biofilm and anti-inflammatory activities. In addition, they demonstrated low toxicity to human cells and were effective in a mouse model of MRSA infection.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Meeting Abstract
Agriculture, Dairy & Animal Science
Mohsen Davoudkhani, Francesco Rubino, Christopher J. Creevey, Rafael Munoz-Tamayo
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Adam J. Mulkern, Linda B. Oyama, Alan R. Cookson, Christopher J. Creevey, Toby J. Wilkinson, Hamza Olleik, Marc Maresca, Giarla C. da Silva, Patricia P. Fontes, Denise M. S. Bazzolli, Hilario C. Mantovani, Bamu F. Damaris, Luis A. J. Mur, Sharon A. Huws
Summary: This study evaluated the therapeutic potential of antimicrobial peptides (AMPs) from the rumen microbiome against Pseudomonas aeruginosa infections. All AMPs exhibited antimicrobial activity against the strains tested, with no decrease in activity. The AMPs Lynronne 1 and 2 showed efficacy in an in vivo infection model. These findings highlight the potential of microbiome-derived AMPs for the treatment of Pseudomonas aeruginosa infections.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biochemistry & Molecular Biology
Charley G. P. McCarthy, Peter O. Mulhair, Karen Siu-Ting, Christopher J. Creevey, Mary J. O'Connell
Summary: There is conflicting evidence regarding whether sponges or comb jellies are at the root of the animal phylogeny, and dataset size, construction, and model fit all influence animal root inference.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Lorenzo A. Santorelli, Toby Wilkinson, Ronke Abdulmalik, Yuma Rai, Christopher J. Creevey, Sharon Huws, Jorge Gutierrez-Merino
Summary: This study investigates the bacterial communities in different beehives and finds that each hive has its own distinct microbiome, which is influenced by plants, beekeeping methods, and the bacterial communities in the surrounding environment. Therefore, the microbiome of beehives can be used as a valuable biosensor to inform the health of honeybees and their surrounding environment.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Agriculture, Dairy & Animal Science
Levente Kovacs, Ferenc Pajor, Mikolt Bakony, Hedvig Febel, Joan E. Edwards
Summary: Butyrate is commonly used as a feed additive to support gut health in pigs, poultry, and young ruminants. However, the effects of precalving butyrate supplementation on dairy cows and their calves have not been extensively studied. This on-farm study found that prepartum magnesium butyrate (MgB) supplementation enhanced colostrum yield and improved various parameters in dairy cows, such as lactation performance, calving ease, fertility, and body condition score. The calves in the MgB-supplemented group also showed increased vitality at birth. These findings highlight the wide range of benefits provided by prepartum MgB supplementation for dairy cows and their newborn calves.
Article
Agriculture, Dairy & Animal Science
Aaron J. Brown, Gillian Scoley, Niamh O'Connell, Alan Gordon, Katie Lawther, Sharon A. Huws, Steven J. Morrison
Summary: Good management of hygiene is required to minimise the risk of disease transmission in pre-weaned calf rearing facilities. In this study, various samples were collected from calf rearing facilities and analysed for hygiene indicators. The results showed that the use of automatic feeders and group pen buckets improved hygiene levels, while self-fill drinkers and single pens had higher chances of containing high levels of bacteria. Cleaning milk feeders after every feed and using group pens with solid floors were also found to be effective in maintaining hygiene levels.
Article
Veterinary Sciences
Hedvig Febel, Joan Edwards, Ferenc Pajor, Viktor Jurkovich, Mikolt Bakony, Levente Kovacs
Summary: Prepartum magnesium butyrate (MgB) supplementation improved lactation performance and reduced inflammation in dairy cows. It increased milk yield, fat and protein concentrations, and decreased milk somatic cell count and inflammation-related protein levels. However, the mechanism by which MgB improves rumination activity remains unclear.
VETERINARY SCIENCES
(2023)
Meeting Abstract
Infectious Diseases
Lucy Dillon, Nicholas J. Dimonaco, Christopher J. Creevey
JAC-ANTIMICROBIAL RESISTANCE
(2023)