Article
Plant Sciences
Yangyang Zhang, Wenjing Zhang, Qicong Cao, Xiaojian Zheng, Jingting Yang, Tong Xue, Wenhao Sun, Xinrui Du, Lili Wang, Jing Wang, Fengying Zhao, Fengning Xiang, Shuo Li
Summary: Soil stress, such as salinity, is a primary factor leading to reduced crop yields worldwide. However, existing tools for studying plant responses to soil stress are inadequate. In this study, a low-cost and high-throughput plant soil cultivation and phenotyping system called WinRoots was developed. This system provides uniform and controlled soil stress conditions and accurately measures the overall phenotypes of plants, including their roots.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Fangyuan Zhou, Xiaoqing Wu, Yunxiao Gao, Susu Fan, Hongzi Zhou, Xinjian Zhang
Summary: This study investigated the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates and predicted the corresponding function of these different root bacterial microbiota. The results showed significant differences in alpha and beta diversity of samples from different substrates, as well as changes in abundance of specific bacterial genera and synthetic pathways in the root microbiome.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Plant Sciences
Yu Xu, Mengjie Zhu, Yibin Feng, Hongxi Xu
Summary: Herbal plant-microbiome interactions play a crucial role in plant growth, health, and the production of bioactive compounds. Understanding these interactions is important for improving the performance and medicinal value of herbal plants.
Article
Environmental Sciences
Jennie Cox, Timothy Stone, Patrick Ryan, Jeff Burkle, Roman Jandarov, Mark J. Mendell, Christine Niemeier-Walsh, Tiina Reponen
Summary: This study aimed to examine and compare environmental microbiota in dust and children's respiratory health outcomes at ages seven and twelve. Various regression models were used to analyze the associations between dust microbiota and respiratory outcomes. The findings suggested that a complex mixture of bacterial and fungal species in indoor environments may play a more significant role in influencing health outcomes than individual species. The Weighted Quantile Sum regression models demonstrated that a combination of species could impact health outcomes, with certain heavily weighted species influencing the models significantly.
ENVIRONMENTAL RESEARCH
(2022)
Article
Food Science & Technology
Hiran Castagnino Kunert-Filho, Thales Quedi Furian, Renata Sesterhenn, Gabriela Zottis Chitolina, Daiane Elisa Willsmann, Karen Apellanis Borges, Carlos Tadeu Pippi Salle, Hamilton Luiz de Souza Moraes, Vladimir Pinheiro do Nascimento
Summary: Poultry products are prone to contamination by microorganisms during the slaughtering process. High-throughput next generation sequencing (HT-NGS) allows for precise and culture-independent assessment of the microbiome in poultry carcasses. Differences in microbiome composition were observed among slaughterhouses, with some unique microorganisms detected in specific establishments. Significant reductions in microbial sequences were found as the slaughtering process progressed, and stricter control procedures were associated with lower contamination. These findings provide valuable insights for ensuring food safety in slaughterhouses.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Review
Biochemical Research Methods
Matteo Chialva, Luisa Lanfranco, Paola Bonfante
Summary: Plants in nature interact closely with microbial communities, which are important for understanding plant responses to microbes and driving microbial community structure and function. Rational engineering of plant microbiota can improve the sustainability of agriculture.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Marion K. Gallus, Rudi F. Vogel, Matthias A. Ehrmann
Summary: This study developed a method for selectively isolating lactic acid bacteria (LAB) from insects, and successfully isolated different species of LAB from Drosophila melanogaster and Tenebrio molitor. The method provides a strategy for studying other niches.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Kristin Aleklett, Daniel Rosa, Brian John Pickles, Miranda M. Hart
Summary: Little is known about the impact of plant life events on the composition of the plant microbiome. This study manipulated the timing of microbial exposure and the priority effects of early colonizers to investigate their effects on the root microbiota in mature plants. The results showed that the timing of soil exposure in the early life stages of a plant plays an important role in the development of the root microbiota in mature plants.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Tri Tran, Elizabeth French, Anjali S. Iyer-Pascuzzi
Summary: The functional traits of bacterial root endophytes can predict their impact on plant growth. This study isolated 183 bacterial endophytes from two tomato species and screened them for six functional traits. The isolates were then grouped based on their traits, and it was found that isolates within the same functional group promoted plant growth at similar levels, regardless of their host origin or taxonomy.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Review
Microbiology
Saber Khelaifia, Pilliol Virginie, Souad Belkacemi, Herve Tassery, Elodie Terrer, Gerard Aboudharam
Summary: Recent years have seen a shift towards culture-dependent approaches in the study of the human microbiota. However, studies on the oral microbiota have been limited. This article presents various methodologies and culture media for studying the oral microbiota through culture, focusing on eukaryota, bacteria, and archaea. The review aims to provide a comprehensive understanding of the oral microbiota's role in oral health and diseases.
Article
Plant Sciences
Manish Tiwari, Baljinder Singh, Manisha Yadav, Vimal Pandey, Sabhyata Bhatia
Summary: Through sequencing and analyzing multiple miRNA and PARE libraries, the regulatory mechanism of miRNAs in chickpea root nodule formation was studied, revealing both conserved and novel miRNAs. Further phylogenetic analysis unveiled the ancestral relationships of these miRNAs. Studying the targeted genes of miRNAs and the changes in nodule numbers laid the foundation for further understanding the nodulation process in chickpea and other leguminous crops.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Biochemical Research Methods
Natalie J. Wu-Woods, Jacob T. Barlow, Florian Trigodet, Dustin G. Shaw, Anna E. Romano, Bana Jabri, A. Murat Eren, Rustem F. Ismagilov
Summary: This study introduces a microbial-enrichment method (MEM) that enables the removal of host DNA in human intestinal biopsies and allows for the characterization of low-abundance microbial taxa. The method provides deeper insights into the high-throughput characterization of the gut microbiome and demonstrates the construction of metagenome-assembled genomes from human intestinal biopsies.
Article
Biochemical Research Methods
Rutan Zhang, Nate K. Ashford, Amy Li, Dylan H. Ross, Brian J. Werth, Libin Xu
Summary: Antimicrobial resistance poses a major threat to human health and the development of new antimicrobials is slow. To study lipid-mediated pathways in antimicrobial-resistant bacteria, a high-throughput method combining liquid chromatography and ion mobility separation was developed for lipidomic analysis using standard 96-well plates. The method was validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from methicillin-resistant Staphylococcus aureus (MRSA) grown in a 96-well plate.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Agronomy
Xinjian Zhang, Chunli Ling, Xiaoqing Wu, Susu Fan, Qingxia Liang, Fangyuan Zhou
Summary: This study investigated the differences in bacterial communities surrounding strawberry roots grown in two artificial substrates and greenhouse soil. The results provide basic information on root bacterial diversity of strawberries grown in different substrates and help to explore beneficial root microorganisms for sustainable strawberry production.
Article
Biochemical Research Methods
Patrick Mueller, Jacobo de la Cuesta-Zuluaga, Michael Kuhn, Maral Baghai Arassi, Tim Treis, Sonja Blasche, Michael Zimmermann, Peer Bork, Kiran Raosaheb Patil, Athanasios Typas, Sarela Garcia-Santamarina, Lisa Maier
Summary: The human gut microbiome plays a vital role in health, and disturbances in its composition are associated with various diseases. Small-molecule xenobiotics, such as drugs and chemical pollutants, can alter the gut microbiota and are recognized as one of the main factors affecting microbiome diversity. This article presents a high-throughput screening protocol that allows for the investigation of the inhibitory effects of hundreds of xenobiotics on anaerobic gut bacteria. The authors have developed an experimental setup and protocol that enables the testing of up to 5,000 compounds on a target gut species within 5 days under strict anaerobic conditions. The protocol can also be modified to test the effects of drugs on microbial communities obtained from stool samples. This protocol is expected to accelerate the study of interactions between small molecules and the gut microbiome, providing a deeper understanding of this microbial ecosystem and its relationship to human health.
Review
Cell Biology
Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai
Summary: This article systematically summarizes the advantages and limitations of methods in microbiome research, recommends specific analysis flows and common software, introduces statistical and visualization methods suitable for microbiome analysis, and provides a reproducible analysis guide. The goal is to help researchers conduct data analysis more effectively and efficiently mine the biological significance behind the data.
Article
Biochemistry & Molecular Biology
Jun Xu, Jie-Ni Zhang, Bo-Hui Sun, Qing Liu, Juan Ma, Qian Zhang, Yong-Xin Liu, Ning Chen, Feng Chen
Summary: Multiple factors, such as genotype, age, diet, and nutrition, affect the gut microbiome. This study investigated the relative capacity of different factors to shape the gut microbiome using a genetic vitamin A-deficient mouse model. The results showed that the depletion of vitamin A in the diet led to changes in the bacterial community, with certain bacteria decreasing while others increased. Age exerted a relatively weaker but longer-lasting influence. These findings suggest that genotype may play a greater role than diet and age in shaping the gut microbiome.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Ecology
Lisa K. Mahdi, Shingo Miyauchi, Charles Uhlmann, Ruben Garrido-Oter, Gregor Langen, Stephan Wawra, Yulong Niu, Rui Guan, Senga Robertson-Albertyn, Davide Bulgarelli, Jane E. Parker, Alga Zuccaro
Summary: Plant root-associated bacteria can protect against pathogen infections, while root endophytic fungi combined with core bacterial members provide synergistic protection. The early growth promotion benefits of these interactions are dependent on the host and microbiota composition, and are associated with modulation of microbial effectors and carbohydrate-active enzymes instead of extensive host transcriptional reprogramming.
Review
Biochemistry & Molecular Biology
Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang, Yang Bai
Summary: This article discusses the research progress of root microbiome, highlighting the importance of studying plant-commensal community. With advanced technologies, we are able to gain a deeper understanding of the interactions between plants and their commensals. The article also points out the impact of soil environment and host plants on commensal community.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Paloma Duran, Jose Flores-Uribe, Kathrin Wippel, Pengfan Zhang, Rui Guan, Barbara Melkonian, Michael Melkonian, Ruben Garrido-Oter
Summary: The study reveals the extensive similarity between the microbiota associated with microscopic algae and the root microbiota of land plants. Both algae and plants attract heterotrophic bacteria by releasing organic compounds and establish symbiotic relationships with them. Furthermore, the assembly process of microbial communities associated with algae and plant roots shares common ecological principles.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Leli Wang, Qihang Liu, Yuwei Chen, Xinlei Zheng, Chuni Wang, Yining Qi, Yachao Dong, Yue Xiao, Cang Chen, Taohong Chen, Qiuyun Huang, Zongzhao Zhai, Cimin Long, Huansheng Yang, Jianzhong Li, Lei Wang, Gaihua Zhang, Peng Liao, Yong-Xin Liu, Peng Huang, Jialu Huang, Qiye Wang, Huanhuan Chu, Jia Yin, Yulong Yin
Summary: A study identified a potentially probiotic strain of Pediococcus in sow milk that confers antioxidant capacity by activating the Nrf2-Keap1 signaling pathway in piglets. The findings provide useful resources for understanding the relationship between maternal microbiota and offspring.
Article
Microbiology
Sunde Xu, Yong-Xin Liu, Tomislav Cernava, Hongkai Wang, Yaqi Zhou, Tie Xia, Shugeng Cao, Gabriele Berg, Xing-Xing Shen, Ziyue Wen, Chunshun Li, Baoyuan Qu, Hefei Ruan, Yunrong Chai, Xueping Zhou, Zhonghua Ma, Yan Shi, Yunlong Yu, Yang Bai, Yun Chen
Summary: This study identified the bacterial microbiome associated with fungal fruiting bodies and discovered an effective bacterium, Pantoea agglomerans ZJU23, that suppresses fungal growth and infection. The study also identified a key antifungal compound, Herbicolin A, secreted by ZJU23, and determined its biosynthetic gene cluster. Herbicolin A demonstrated potent efficacy against various fungal pathogens both in vitro and in planta, and showed a distinct mode of action. Additionally, Herbicolin A exhibited higher activity against human opportunistic fungal pathogens than clinically used fungicides.
NATURE MICROBIOLOGY
(2022)
Correction
Microbiology
Rong-min Zhang, Jian Sun, Ruan-yang Sun, Min-ge Wang, Chao-yue Cui, Liang-xing Fang, Mei-na Liao, Xiao-qing Lu, Yong-xin Liu, Xiao-Ping Liao, Ya-Hong Liu
MICROBIOLOGY SPECTRUM
(2022)
Article
Engineering, Environmental
Dongdan Yuan, Lei Zheng, Yong-Xin Liu, Hongguang Cheng, Aizhong Ding, Xiaomin Wang, Qiuyang Tan, Xue Wang, Yuzi Xing, En Xie, Haoming Wu, Shanyun Wang, Guibing Zhu
Summary: Through the use of double tracer technique and metagenomic sequencing, we found that the production of N2O in plateau wetlands is promoted by nitrifier denitrification, with the key functional genes belonging to comammox bacteria Nitrospira nitrificans. The comammox bacterial species N. nitrificans and ammonia oxidizing bacterial species Nitrosomonas europaea cooperate to produce N2O in plateau wetland sediments. Environmental factors such as elevation and total organic matter influence the cooperation pattern via N. nitrificans, thus affecting N2O production activity in plateau wetland sediments.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Agronomy
Jiao Xi, Zanbo Ding, Tengqi Xu, Wenxing Qu, Yanzhi Xu, Yongqing Ma, Quanhong Xue, Yongxin Liu, Yanbing Lin
Summary: This study successfully reduced the parasitism of O. cumana and promoted sunflower growth by combining the use of fermentation filtrates and crop rotation. Additionally, this combined method also affected the bacterial community composition of sunflower rhizosphere.
Editorial Material
Cell Biology
Yunyun Gao, Danyi Li, Yong-Xin Liu
Review
Cell Biology
Tao Wen, Guoqing Niu, Tong Chen, Qirong Shen, Jun Yuan, Yong-Xin Liu
Summary: With the advancement of sequencing technology, numerous microbiome studies have been published, leading to the development of related analysis tools. This study organizes and classifies 324 common R packages for microbiome analysis, which can assist researchers in quickly finding suitable tools for their analysis.
Article
Agronomy
Wen Luo, Yuanli Li, Ruiping Luo, Gehong Wei, Yongxin Liu, Weimin Chen
Summary: This study revealed that dodder parasitism significantly influenced the fungal communities and secondary metabolites in soybean roots. The composition and diversity of fungal communities in the rhizosphere and endosphere of soybean were altered by parasitism, with an increase in the relative abundance of potential pathogenic fungus Alternaria in the root endosphere. Soil total nitrogen content was positively correlated with the abundance of Alternaria in the rhizosphere and endosphere. Metabolomic analysis showed that dodder parasitism led to changes in flavonoid accumulation in soybean roots, with an upregulation of kaempferol and its derivatives. This study highlights the important role of dodder parasitism in shaping fungal communities and secondary metabolites associated with soybean roots.
Article
Agronomy
Yuanping Zhou, Wenjiao Luo, Maoxing Li, Qiong Wang, Yongxin Liu, Huachun Guo
Summary: Growing potatoes in idle rice fields through the rice-potato rotation system can improve food security and suppress soilborne fungal pathogens.