Article
Microbiology
Jason A. Rothman, Jenna L. Riis, Katrina R. Hamilton, Clancy Blair, Douglas A. Granger, Katrine L. Whiteson
Summary: Human oral microbial communities have significant implications for oral and systemic health due to their diversity. Understanding the differences between healthy and dysbiotic oral microbiomes is important, especially within and between families. This study investigates the changes in oral microbiome composition within individuals and the impact of factors such as environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. The findings reveal differences in oral microbiomes between children and caregivers, with shared diversity but distinct differences, and highlight the associations between the oral microbiome and various salivary markers.
Article
Microbiology
Ya Wang, Kelsey N. Thompson, Yan Yan, Meghan I. Short, Yancong Zhang, Eric A. Franzosa, Jiaxian Shen, Erica M. Hartmann, Curtis Huttenhower
Summary: Characterization of microbial activity is important for understanding the basic biology of microbial communities. Current sequence-based technologies can't differentiate microbial activity well, leading to incomplete understanding of microbial community structures and transmission mechanisms. 16S-RNA-seq has been proposed as a potential solution, but its efficacy has not been systematically evaluated. This study evaluated the viability assessment ability of 16S-RNA-seq in synthetic and complex microbial communities.
Article
Microbiology
Gleyciane Machado da Costa, Savio Souza Costa, Rafael Azevedo Barauna, Bruno Pureza Castilho, Izabel Cruz Pinheiro, Artur Silva, Ana Paula Schaan, Andrea Ribeiro-dos-Santos, Diego Assis das Gracas
Summary: The study reveals that human activities, such as the construction of a highway, have impacted the microbial communities in the Amazonian mangroves and resulted in a loss of biodiversity.
Article
Plant Sciences
Chakrit Bunyoo, Peerapat Roongsattham, Sirikorn Khumwan, Juthaporn Phonmakham, Passorn Wonnapinij, Arinthip Thamchaipenet
Summary: This study investigated the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions using 16S rRNA amplicon sequencing. The results showed that Proteobacteria was the dominant phylum in duckweed samples. A total of 24 microbial genera were identified as a core microbiome, with consistent proportions across all duckweed subtypes. The diversity of microbial communities decreased after nutrient-deficient stress, but the relative abundance of certain genera significantly increased. Functional prediction of the metagenome data revealed enrichment of essential pathways involved in DAB colonization and biodegradation under stress condition.
Article
Biochemistry & Molecular Biology
Seeu Si Ong, Jia Xu, Choon Kiat Sim, Alexis Jiaying Khng, Peh Joo Ho, Philip Kam Weng Kwan, Aarthi Ravikrishnan, Kiat-Tee Benita Tan, Qing Ting Tan, Ern Yu Tan, Su-Ming Tan, Thomas Choudary Putti, Swee Ho Lim, Ee Ling Serene Tang, Niranjan Nagarajan, Neerja Karnani, Jingmei Li, Mikael Hartman
Summary: This study investigated the microbial flora in patients with idiopathic granulomatous mastitis (IGM) and lactational mastitis (LM). The results showed differences between IGM pus samples and corresponding skin samples, while no significant differences were observed in LM samples. There was no characteristic dominant genus in IGM samples, but Corynebacterium kroppenstedtii showed higher levels in IGM pus samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Marcel Suleiman, Francesca Demaria, Cristina Zimmardi, Boris Alexander Kolvenbach, Philippe Francois-Xavier Corvini
Summary: Pharmaceuticals accumulation in the environment is a concern for our planet and health. Little is known about the biodegradation capacity of microbial communities for multiple micropollutants. This study demonstrates the feasibility of cultivating stable microbial communities capable of degrading a mixture of highly concentrated pharmaceuticals.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Marcelle Muniz Barreto, Maren Ziegler, Alexander Venn, Eric Tambutte, Didier Zoccola, Sylvie Tambutte, Denis Allemand, Chakkiath Paul Antony, Christian R. Voolstra, Manuel Aranda
Summary: Ocean warming and acidification, direct consequences of climate change, affect coral reefs worldwide. This study found that ocean acidification has stronger effects on the active microbial community associated with corals, compared to the resident community. The results suggest that rDNA- and rRNA-based sequencing are complementary tools for investigating the effects of environmental change on microbial assemblage structure and activity.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Markus Haber, Dalit Roth Rosenberg, Maya Lalzar, Ilia Burgsdorf, Kumar Saurav, Regina Lionheart, Yoav Lehahn, Dikla Aharonovich, Laura Gomez-Consarnau, Daniel Sher, Michael D. Krom, Laura Steindler
Summary: This study investigated the temporal and spatial patterns of bacterial and archaeal communities in the Eastern Mediterranean Sea. The results showed that oligotrophic bacteria dominated the microbial community throughout the year, and seasons significantly affected the community composition. Although the dominant taxa remained consistent over the two-year sampling period, their dominance varied. While station location did not have an overall effect on the microbial community, the most coastal site differed significantly from the offshore stations in certain seasons.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
L. G. Schaerer, P. N. Webb, A. Corazzola, W. C. Christian, S. M. Techtmann
Summary: This study found that sources other than water can impact the microbial community of a boat, indicating that terrestrial micro-organisms may influence the boat microbial community.
JOURNAL OF APPLIED MICROBIOLOGY
(2021)
Article
Environmental Sciences
Xiao Xiao, Ya-Li Zhang, Zi-An Zhou, Fan Wu, Hou-Feng Wang, Xin Zong
Summary: This study investigates how microbial communities in lake sediments respond to different concentrations of PAC and finds that PAC treatment can greatly affect the microbial diversity and structure in lake sediments, as well as the functional pathways. The results highlight the potential impact of chemical phosphorus removing reagents on the environment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Celine Lavergne, Polette Aguilar-Munoz, Natalia Calle, Frederic Thalasso, Maria Soledad Astorga-Espana, Armando Sepulveda-Jauregui, Karla Martinez-Cruz, Laure Gandois, Andres Mansilla, Rolando Chamy, Maialen Barret, Lea Cabrol
Summary: Freshwater ecosystems play a significant role in methane emissions and this study investigated the effects of temperature on microbial community structure and methane production pathways in sub-Antarctic lake sediments. The research found that temperature had a significant impact on methane production rates, particularly when methanogenic precursors such as acetate and H-2/CO2 were introduced.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Environmental Sciences
Bo Zhang, Zhi-Ling Li, Cai-Hua Bai, Jing-Lan Liu, Jun Nan, Di Cao, Li-Wei Li
Summary: This study analyzed 10 groundwater samples for their nitrate, nitrite, COD, and sulfate concentrations, and characterized their microbial compositions using 16 S rRNA based high-throughput sequencing methods. The results showed that the microbial structures of groundwater samples with nitrate concentrations higher than the maximum contamination level (MCL) were significantly different from those with lower nitrate concentrations. Furthermore, JG30-KM-CM45, Sphingomonas, and Rhodococcus were found to be closely correlated with nitrate concentration.
ENVIRONMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Asmus Olesen, Rafel Pinilla-Redondo, Mads Hansen, Jakob Russel, Arnaud Dechesne, Barth F. Smets, Jonas Madsen, Joseph Nesme, Soren Sorensen
Summary: Horizontal gene transfer plays a crucial role in spreading antibiotic resistance genes among pathogens. Plasmids, such as IncHI1A, are believed to facilitate the dissemination of resistance genes. The microbial community in urban wastewater treatment plants is highly permissive for the transfer of plasmids. Our study shows that both pB10 and R27 plasmids readily transfer within these communities, including to members of different bacterial families and even phyla. This suggests that HI1A plasmids facilitate gene transfer not only within Enterobacteriaceae, but also between different families of Gammaproteobacteria.
Article
Environmental Sciences
Giorgia Palladino, Elena Biagi, Simone Rampelli, Margherita Musella, Federica D'Amico, Silvia Turroni, Patrizia Brigidi, Gian Marco Luna, Marco Candela
Summary: The study reveals that the microbial community associated with the jewel anemone Corynactis viridis undergoes significant changes across different seasons, shifting its ecological structure from oligotrophic anaerobic to heterotrophic ecosystem. These microbial communities are unique and distinct from those in the surrounding seawater.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biodiversity Conservation
Hao Liao, Xiuli Hao, Fei Qin, Manuel Delgado-Baquerizo, Yurong Liu, Jizhong Zhou, Peng Cai, Wenli Chen, Qiaoyun Huang
Summary: Microbial communities have critical roles in fixing carbon from the atmosphere and fixing it in the soils, but their large-scale variations and drivers are poorly understood. This study conducted a large-scale survey in China and found that soil autotrophic organisms, such as bacteria and protists, are crucial for explaining CO2 fluxes from the atmosphere to soils. The fixation rates of CO2 were significantly correlated to the variations in autotrophic bacteria and phototrophic protists.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Ecology
Lu Zhang, Xinyu Huang, Jizhong Zhou, Feng Ju
Summary: This study uses stable isotope probing to identify diverse uncultivated predatory bacteria in activated sludge microbiota and finds Myxococcota species to be prevalent and potentially influential in wastewater treatment processes.
Article
Ecology
Tao Xu, Xuanyu Tao, Hongxi He, Megan L. Kempher, Siping Zhang, Xiaochun Liu, Jun Wang, Dongyu Wang, Daliang Ning, Chongle Pan, Honghua Ge, Nannan Zhang, Yong-Xing He, Jizhong Zhou
Summary: Carbohydrate utilization is critical for microbial survival. The phosphotransferase system (PTS) is a well-known microbial system involved in carbohydrate metabolism, but its role in non-model prokaryotes remains underexplored. In this study, the prevalence of incomplete PTSs in prokaryotes was investigated, and lignocellulose-degrading clostridia was found to have lost PTS sugar transporters and carry a substitution in the core PTS component. Functional and structural diversification of PTS components were observed, providing novel insights into the regulatory mechanisms of incomplete PTSs.
Article
Environmental Sciences
Ke Shi, Bin Liang, Kai Feng, Daliang Ning, Carolyn R. Cornell, Yanqing Zhang, Wenbin Xu, Min Zhou, Ye Deng, Jiandong Jiang, Tiejun Liu, Aijie Wang, Jizhong Zhou
Summary: Electrostimulated hydrolysis acidification (eHA) is an efficient wastewater pretreatment biotechnology that accelerates the removal of refractory pollutants by affecting microbial interspecies associations. This study investigated the principles of cross-niche microbial associations and community assembly using molecular ecological network and phylogenetic bin-based null model analysis. The results showed that electrostimulation significantly increased the degradation efficiency of organic nitrogen pollutants and altered the microbial community composition and structure. Electroactive bacteria were enriched in the electrode biofilm, while functional degraders were enriched in the planktonic sludge. Electrostimulation also strengthened the synergistic microbial associations between sludge and biofilm members, and deterministic assembly became more important. This study enhances our understanding of the manipulation of sludge microbiomes in engineered wastewater treatment systems.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Engineering, Environmental
Ke Shi, Haoyi Cheng, Carolyn R. Cornell, Haiwei Wu, Shuhong Gao, Jiandong Jiang, Tiejun Liu, Aijie Wang, Jizhong Zhou, Bin Liang
Summary: Improving the degradation of refractory nitrogen-containing organics is essential for meeting nitrogen standards and ensuring aquatic ecology safety. This study demonstrated that micro-aerobic conditions and electrogenic respiration can significantly enhance ammonification through the degradation of aniline, an amination product of nitrobenzene. The results showed that aerobic aniline degraders and electroactive bacteria were enriched in suspension and inner electrode biofilm, respectively, and network analysis revealed a positive association between aniline degraders and electroactive bacteria.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Limnology
Yu Wang, Rui Zhang, Yunfeng Yang, Qichao Tu, Jizhong Zhou, Nianzhi Jiao
Summary: Ocean acidification significantly changes the metabolism and structure of plankton communities in the ocean. Evaluating the response of marine bacterioplankton to acidification is important for understanding future biogeochemical processes in the ocean. However, the influence of acidification on the functional diversity of bacterioplankton is still unclear.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Plant Sciences
Meitong Jiang, Manuel Delgado-Baquerizo, Mengting Maggie Yuan, Jixian Ding, Etienne Yergeau, Jizhong Zhou, Thomas W. Crowther, Yuting Liang
Summary: This study found that native microbial strains originating from typical agricultural soils can promote maize growth better than commercial plant growth-promoting rhizobacteria in soils with different fertility. The colonization and positive interaction with resident microbial communities contribute to the superior performance of native strains. These findings suggest that engineering crop microbiomes using native microbes could improve food production in poor soils.
Article
Microbiology
Dongyu Wang, Kristopher A. Hunt, Pieter Candry, Xuanyu Tao, Neil Q. Wofford, Jizhong Zhou, Michael J. McInerney, David A. Stahl, Ralph S. Tanner, Aifen Zhou, Mari Winkler, Chongle Pan
Summary: A synthetic community consisting of four microbial species was designed to carry out key metabolic processes in anaerobic degradation. The interactions between microorganisms were observed, such as cross-feeding and competition. This study revealed positive and negative synergies among multiple microorganisms and provided insights into the impact of environmental perturbations on microbial interactions.
Article
Microbiology
Qi-Yun Liang, Jin-Yu Zhang, Daliang Ning, Wen-Xing Yu, Guan-Jun Chen, Xuanyu Tao, Jizhong Zhou, Zong-Jun Du, Da-Shuai Mu
Summary: Inhibiting sulfate-reducing bacteria (SRB) has shown various effects on microbial community properties and coexistence patterns, indicating the importance of SRB in organic matter (OM) degradation. Suppression of SRB resulted in decreased relative abundances of several bacterial families and altered network and community assembly processes. These findings highlight the essential role of SRB in OM degradation.
Article
Microbiology
Mengzhi Ji, Xiangyu Fan, Carolyn R. Cornell, Ya Zhang, Mengting Maggie Yuan, Zhen Tian, Kaili Sun, Rongfeng Gao, Yang Liu, Jizhong Zhou
Summary: This study investigated the responses of viral communities and functional genes to experimental warming in the Alaskan permafrost region. The results showed that environmental conditions, such as nitrogen and carbon content, and soil thawing duration, significantly influenced the composition and abundance of viral communities and functional genes. The study also revealed that viruses can manipulate microbial communities at different soil depths through different infection strategies, which may be one of the major factors causing differences in microbial responses to warming.
Article
Environmental Sciences
Ya Zhang, Daliang Ning, Linwei Wu, Mengting Maggie Yuan, Xishu Zhou, Xue Guo, Yuanliang Hu, Siyang Jian, Zhifeng Yang, Shun Han, Jiajie Feng, Jialiang Kuang, Carolyn R. Cornell, Colin T. Bates, Yupeng Fan, Jonathan P. Michael, Yang Ouyang, Jiajing Guo, Zhipeng Gao, Zheng Shi, Naijia Xiao, Ying Fu, Aifen Zhou, Liyou Wu, Xueduan Liu, Yunfeng Yang, James M. Tiedje, Jizhong Zhou
Summary: The authors investigated the response of Archaea to experimental warming in a tallgrass prairie ecosystem and found that warming led to reduced diversity and convergent succession in the archaeal community. They also observed changes in ecosystem function. Although stochastic processes dominated community changes, their importance decreased over time. This study highlights the importance of understanding the temporal succession of ecological communities and the mechanisms underlying their responses to climate warming. The findings provide insights into the response of the Archaea domain to warming, which is still poorly understood.
NATURE CLIMATE CHANGE
(2023)
Article
Microbiology
Qiannan Peng, Lu Lin, Qichao Tu, Xiaopeng Wang, Yueyue Zhou, Jiyu Chen, Nianzhi Jiao, Jizhong Zhou
Summary: This study demonstrates the impacts of different lignocellulose substrates and exposure times on long-term bacterial community assembly and identifies comprehensive potential decomposers at the levels of taxa and functional genes. The links between ligninolytic functional traits and taxonomic groups of substrate-specific populations are revealed. It shows that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.
Article
Food Science & Technology
Chaoyang Liu, Meitong Jiang, Mengting Maggie Yuan, Ertao Wang, Yang Bai, Thomas W. Crowther, Jizhong Zhou, Zhiyuan Ma, Li Zhang, Yu Wang, Jixian Ding, Wuxing Liu, Bo Sun, Renfang Shen, Jiabao Zhang, Yuting Liang
Summary: This study identifies aluminium-resistant bacteria and their potential contribution to increased rice yields in acidic soils. The synthetic community composed of highly Al-resistant bacterial strains harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation.
Article
Biochemistry & Molecular Biology
Wangsuo Liu, Zhanjun Wang, Ying Tian, Bo Ji
Summary: In this study, we sequenced, assembled, and annotated the complete chloroplast genome of Vincetoxicum mongolicum and compared its highly variable gene regions and phylogenetic positions with other related species. Results showed that the complete cp genome of V. mongolicum was 160,157 bp in length, containing a large single copy region, a pair of inverted repeats region, and a small single copy region. By comparing and analyzing the variable region of the cp gene, several fragments were identified as potential DNA barcodes for distinguishing V. mongolicum and its relatives. Maximum-likelihood phylogenetic tree analysis revealed the evolutionary relationship between V. mongolicum and V. pycnostelma.
GENETICS AND MOLECULAR BIOLOGY
(2023)
Article
Microbiology
Yujia Qin, Liyou Wu, Qiuting Zhang, Chongqin Wen, Joy D. Van Nostrand, Daliang Ning, Lutgarde Raskin, Ameet Pinto, Jizhong Zhou
Summary: Amplicon sequencing of targeted genes is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases can affect the accuracy of results. In this study, a systematic analysis was conducted using a mock community to identify the sources of artifacts and test different approaches to improve sequencing accuracy. The results showed that chimeric sequences were a major source of artifacts, which were significantly correlated with the GC content of the targeted sequences. The study also found that amplification bias could occur due to primer affinity differences. The insights from this study can help enhance the quality of amplicon sequencing studies and improve data analysis approaches.
