Article
Microbiology
Iva Stojan, Zeljka Trumbic, Ivana Lepen Pleic, Danijela Santic
Summary: Recent advances in molecular biology methods and next-generation sequencing have revolutionized metabarcoding studies on microbial communities. This study assessed the influence of five DNA extraction methods on community composition and DNA yield, finding significant differences in community structure and the importance of rare taxa. Direct PCR represents an interesting alternative, but caution is needed in method selection and consistent application.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Gertrude Wegl, Nikolaus Grabner, Andreas Kostelbauer, Viviana Klose, Mahdi Ghanbari
Summary: Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is crucial for managing and manipulating microbial communities. A systematic comparison of sample preservation and DNA extraction approaches for pig and chicken microbiota samples showed that these technical steps can significantly affect microbial community structure, with effects varying by sample type. Standardization is essential for accelerating progress in livestock microbiota research.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Natthaya Chuaypen, Thananya Jinato, Anchalee Avihingsanon, Sakkarin Chirapongsathorn, Supapon Cheevadhanarak, Intawat Nookaew, Yasuhito Tanaka, Pisit Tangkijvanich
Summary: The study found that direct-acting antivirals can improve gut microbiota dysbiosis in HCV-infected patients, with reduced microbial diversity and Firmicutes-Bacteroidetes ratio in those with HIV coinfection. Responders achieving sustained virological response showed better recovery of gut microbiota after treatment.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Klaudia Tutka, Magdalena Zychowska, Anna Zaczek, Karolina Maternia-Dudzik, Jakub Pawelczyk, Dominik Strapagiel, Jakub Lach, Adam Reich
Summary: This study evaluated the diversity and composition of the bacterial microbiome in PN lesions and found that the abundance of Staphylococcus was significantly higher in samples from PN and AD patients compared to controls. The microbiome composition in PN was highly similar to that of AD. These findings suggest a potential role of the microbiome in the pathogenesis of PN.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cardiac & Cardiovascular Systems
Theda U. P. Bartolomaeus, Till Birkner, Hendrik Bartolomaeus, Ulrike Loeber, Ellen G. Avery, Anja Maehler, Daniela Weber, Bastian Kochlik, Andras Balogh, Nicola Wilck, Michael Boschmann, Dominik N. Mueller, Lajos Marko, Sofia K. Forslund
Summary: DNA extraction methods have a significant impact on the variability of observed microbiome, comparable to interindividual differences, potentially mimicking microbiome signatures of health and nutrition factors. Collection methods have a relatively small influence on microbiome composition. This study provides insight into technical variables to standardize microbiome quantification procedures in clinical research.
CARDIOVASCULAR RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Lilian Lopez Leyva, Nicholas J. B. Brereton, Kristine G. Koski
Summary: Human milk is recognized as the ideal food for infants, providing unique nutritional and immune properties, as well as serving as an important source of bacteria for infants. Research into the human milk microbiome indicates that there is still much to learn about its origins, composition, and functions. Factors such as maternal influences, diet, lifestyle, and location are believed to impact the diversity and composition of the milk microbiome, with advancements in research methods shaping our understanding of this complex ecosystem.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Environmental Sciences
Aoyun Li, Yajing Wang, Yuanyuan He, Bingxian Liu, Mudassar Iqbal, Khalid Mehmood, Tariq Jamil, Yung-Fu Chang, Lianmei Hu, Ying Li, Jianying Guo, Jiaqiang Pan, Zhaoxin Tang, Hui Zhang
Summary: Fluorine and its compounds from industrial production and coal combustion can cause contamination of air, water, and soil, posing a threat to public health through accumulation in animals, plants, and humans via food chain. Exposure to fluoride resulted in damaged intestinal structure and altered gut microbial composition in ducks.
Article
Biotechnology & Applied Microbiology
Shoichiro Kameoka, Daisuke Motooka, Satoshi Watanabe, Ryuichi Kubo, Nicolas Jung, Yuki Midorikawa, Natsuko O. Shinozaki, Yu Sawai, Aya K. Takeda, Shota Nakamura
Summary: The study compared 192 Japanese volunteers' fecal 16S analysis data using modified V1-V2 and standard V3-V4 primers. Results showed that the bacterial composition derived from the V34 region might differ from the actual abundance, suggesting that the modified V12 primer set is more desirable for analyzing the Japanese gut microbiota.
Article
Neurosciences
Wei Cui, Li Xu, Lin Huang, Yang Tian, Yan Yang, Yamei Li, Qian Yu
Summary: The study aims to explore the characteristics of gut microbiota changes over time after stroke. The researchers compared the clinical data and gut microbiota of stroke patients and healthy subjects in two phases. The results showed that gut dysbiosis still existed in patients in the subacute phase and convalescent phase of stroke, and gradually improved with the recovery of stroke. There is a strong correlation between gut microbiota and cognitive function after stroke.
CNS NEUROSCIENCE & THERAPEUTICS
(2023)
Article
Medicine, Research & Experimental
Rui-zhi Yang, Min Liang, Song Lin, Jing Weng, Jia-min Hu, Shi-zhu Lin, Xiao-dan Wu, Kai Zeng
Summary: This study investigated the effect of general anesthetics on the lung microbiome and found that continuous inhalation of isoflurane altered the diversity and composition of the lung microbiota in rats, resulting in post-anesthesia depression.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Parasitology
Haiming Cai, Shengjun Luo, Qihong Liu, Qingfeng Zhou, Zhuanqiang Yan, Zhen Kang, Shenquan Liao, Juan Li, Minna Lv, Xuhui Lin, Junjing Hu, Shuilan Yu, Jianfei Zhang, Nanshan Qi, Mingfei Sun
Summary: This study evaluated the effects of BLES and coccidiosis vaccine in modulating the intestinal microbiome and found that the combination of BLES and coccidiosis vaccine can improve growth performance, alleviate clinical manifestations, and induce favorable alterations to the intestinal microbiota in broiler chickens affected by coccidiosis.
PARASITES & VECTORS
(2023)
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
Biotechnology & Applied Microbiology
Shuangshuang Wang, Feng Song, Haoyu Gu, Zhilong Shu, Xiaowen Wei, Ke Zhang, Yuxiang Zhou, Lanrui Jiang, Zefei Wang, Jienan Li, Haibo Luo, Weibo Liang
Summary: This study investigated the gut microbiota of healthy adults with different traits. The results showed differences in gut microbiota composition between male and female subjects. Additionally, the gut microbiota composition was able to distinguish between different BMI groups. At the phylum level, specific phyla were found to be increased in different BMI groups for both males and females. At the genus level, several distinct genera were identified across BMI groups. The accuracy of predicting body type using a linear regression model was 74%.
MICROBIAL CELL FACTORIES
(2022)
Review
Infectious Diseases
Kristien Nel Van Zyl, Siphiwe R. Matukane, Bianca L. Hamman, Andrew C. Whitelaw, Mae Newton-Foot
Summary: Antibiotic use can alter the diversity and composition of the human microbiota. This systematic review found that certain antibiotics can cause long-term dysbiosis in the microbiome. The importance of longitudinal analysis and studies in pediatric populations was highlighted.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Article
Respiratory System
Rune Nielsen, Yaxin Xue, Inge Jonassen, Ingvild Haaland, Oyvind Kommedal, Harald G. Wiker, Christine Drengenes, Per S. Bakke, Tomas M. L. Eagan
Summary: The study found that the lower airway microbiome varies between examinations, but there is compositional stability within an individual, supporting the idea of a transient airway microbiota with a potentially more stable individual core microbiome.
BMC PULMONARY MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Cornelius Nel, Phillip Gurman, Andrew Swan, Julius van der Werf, Margaretha Snyman, Kennedy Dzama, Klint Gore, Anna Scholtz, Schalk Cloete
Summary: This study evaluated the genetic structure of sheep breeds in South Africa and Australia. The results showed high genetic complexity and diversity in these breeds. The relatedness and divergence varied among different breeds and bloodlines. The study also found that population structure could have an important impact on the compatibility of genomic data.
Article
Agriculture, Dairy & Animal Science
P. T. Muvhali, M. Bonato, I. A. Malecki, S. W. P. Cloete
Summary: This study evaluated monthly egg production and average egg weight for female ostriches and estimated the genetic parameters for these traits. The results showed that egg production had high variability compared to egg weight, and there was no genetic correlation between the two traits.
JOURNAL OF APPLIED POULTRY RESEARCH
(2022)
Article
Multidisciplinary Sciences
Mads F. Schou, Anel Engelbrecht, Zanell Brand, Erik Svensson, Schalk Cloete, Charlie K. Cornwallis
Summary: Research suggests that ostriches have the evolutionary potential to cope with temperature fluctuations, but there is a negative genetic correlation between heat and cold tolerance, which limits their ability to adapt to fluctuating temperatures.
Article
Evolutionary Biology
Kristina L. Paxton, Loren Cassin-Sackett, Carter T. Atkinson, Elin Videvall, Michael G. Campana, Robert C. Fleischer
Summary: The rise in new and emerging infectious diseases poses a threat to human and wildlife health. The introduction of Plasmodium relictum and its mosquito vector to the Hawaiian archipelago has caused significant losses in endemic Hawaiian forest bird species. Understanding the evolution of disease immunity is important for the remaining bird species residing in high elevation habitats. This study compares the gene expression profiles of infected and uninfected birds, providing insights into the molecular pathways involved in survival or mortality during malaria infection.
JOURNAL OF HEREDITY
(2023)
Article
Evolutionary Biology
Elin Videvall, Hanna M. Bensch, Anel Engelbrecht, Schalk Cloete, Charlie K. Cornwallis
Summary: Coprophagy, a behavior observed in various species including birds and mammals, involves the consumption of feces. This study investigates the effects of ostrich chicks ingesting adult feces on their gut microbiota development, growth, feeding behavior, pathogen abundance, and mortality. The results show that coprophagy leads to significant changes in the juvenile gut microbiota, promotes growth, alters feeding behavior, reduces a common gut pathogen, and lowers mortality associated with gut disease.
Article
Agriculture, Dairy & Animal Science
M. Teubes, S. W. P. Cloete, K. Dzama, A. J. Scholtz
Summary: This study estimated the genetic and environmental parameters of tail length, birth weight, and docking weight in a South African Merino flock. The findings suggest that selecting for shorter tails may reduce size if breeding values are not adjusted for docking weight. Further research is needed to explore the genetic basis of tail length and its genetic correlations with other economically important traits.
ANIMAL PRODUCTION SCIENCE
(2023)
Article
Environmental Sciences
Elin Videvall, Pablo Burraco, German Orizaola
Summary: Radioactive contamination has the potential to damage DNA and other biomolecules. A study on animals in Chernobyl revealed that wildlife can persevere despite chronic radiation exposure. However, the effects of radiation on microbial communities in the environment are not well understood. This study examined the impact of ionizing radiation on the diversity and composition of microbiomes in the wetlands of Chernobyl.
ENVIRONMENTAL POLLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Cornelius Nel, Phillip Gurman, Andrew Swan, Julius van Der Werf, Margaretha Snyman, Kennedy Dzama, Willem Olivier, Anna Scholtz, Schalk Cloete
Summary: This study compared the predictive ability of pedigree BLUP and single-step genomic BLUP for production and reproduction traits in South African Merinos. The results showed that single-step genomic BLUP increased the accuracy of prediction for almost all traits, even with a modestly sized reference population. However, the overall accuracy was lower in the cross-flock validation, with greater differences between ABLUP and ssGBLUP.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
P. G. Theron, T. S. Brand, S. W. P. Cloete, J. H. C. van Zyl
Summary: This study used a simple mathematical model to predict the optimal point of slaughter for lamb based on fat depth, and monitored and fitted different genotypic groups. The results showed that linear fitting of fat depth to age and live weight provided the best fit, ewes deposited fat faster than rams, and Dorper crosses had the highest fat deposition rate.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Agriculture, Dairy & Animal Science
P. G. Theron, T. S. Brand, S. W. P. Cloete, J. H. C. van Zyl
Summary: This study aimed to develop genotype-specific feed intake models for South African feedlot lambs. The cumulative intake model was found to accurately predict feed intake and showed a strong correlation with feed conversion ratio.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Agriculture, Dairy & Animal Science
M. R. Kekana, A. Engelbrecht, M. Bonato, S. W. P. Cloete
Summary: The domestication and commercialisation of ostrich farming in South Africa started in the 19th century for feather production. Ostrich feathers, unique and valued for their different attributes compared to other bird feathers, were the primary product until the feather market collapsed in 1914. This review summarises current knowledge on ostrich feather production and research, as the industry has regained importance in South Africa and supplies most of the feathers used worldwide.
WORLDS POULTRY SCIENCE JOURNAL
(2023)
Article
Genetics & Heredity
Homa Papoli Yazdi, Colin Olito, Takeshi Kawakami, Per Unneberg, Mads F. Schou, Schalk W. P. Cloete, Bengt Hansson, Charlie K. Cornwallis
Summary: Sex chromosomes have often evolved with extreme size differences due to degeneration, but in some lineages, ancient sex chromosomes have not degenerated. In ostriches, the W chromosome remains large despite being ancient. By analyzing the ostrich genome, researchers found that recombination rate in the pseudoautosomal region (PAR) is higher than autosomes in females, which slows down degeneration. Genetic variation in the sex-linked region (SLR) is lower than in the PAR, while variation in the PAR is similar to autosomes, suggesting high recombination near the boundaries of the PAR prevents linkage with the SLR. The potential for sexually antagonistic alleles to drive degeneration is limited in ostriches.
Article
Agriculture, Dairy & Animal Science
C. L. Nel, Y. Steyn, A. R. Gilmour, D. Waters, S. A. Clark, J. H. J. van der Werf, A. A. Swan, K. Dzama, S. W. P. Cloete
Summary: Research suggests that cold-stress adaptation may contribute to the genetic trends for survival of lambs. However, the failure to account for the genotype by environment component may lead to underestimation of the heritability of survival traits. It is recommended to conduct larger studies to further explore the effects of cold stress on lamb survival.
ANIMAL PRODUCTION SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Nicholas M. Fountain-Jones, Tatiana Giraud, Lucie Zinger, Holly Bik, Simon Creer, Elin Videvall
Summary: This article explores the common challenges, methodological advancements, and future directions in microbiome research. Key research areas include the drivers of microbiome community assembly, the relationship between microbiome composition and host genetics, microbial functions and spatial partitioning, and understanding non-bacterial components of the microbiome. Methodological advancements such as quantifying absolute abundances, sequencing complete genomes, and novel statistical approaches are useful tools for studying microbial diversity patterns.