Article
Environmental Sciences
Felipe A. S. Barbosa, Leonardo A. S. Brait, Felipe Hernandes Coutinho, Camilo M. Ferreira, Eduardo Freitas Moreira, Lucas de Queiroz Salles, Pedro Milet Meirelles
Summary: Aquifers are of great importance for society, economy, and ecology as they provide a significant portion of the world's freshwater supply. Analyzing microbial communities in different aquifers can help detect and predict environmental impacts. It was found that aquifer categories and low-abundant candidate taxa are strong predictors of microbial community structure.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Endocrinology & Metabolism
Jiachong Liang, Sikandar Ali, Chunrong Lv, Hongyuan Yang, Xiaoqi Zhao, Xiaojun Ni, Chunyan Li, Baiji Danzeng, Yajing Wang, Guobo Quan
Summary: In this study, 16S rDNA sequencing and metagenomic strategy were used to identify fecal bacteria in lactating ewes fed with different levels of dietary proteins. The results showed that the levels of dietary proteins had a significant impact on the populations and genes of fecal bacteria. This study could contribute to the development of a dietary formula for lactating ewes to optimize their growth and health.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Engineering, Environmental
Bridget Hegarty, Zihan Dai, Lutgarde Raskin, Ameet Pinto, Krista Wigginton, Melissa Duhaime
Summary: Viruses play an important role in microbial community ecology and evolution, but their effects in many environments, including drinking water systems, are still largely unknown. This study analyzed viral DNA sequences from drinking water metagenomes from six countries and found that environmental conditions and sample processing influenced viral composition. The use of free chlorine as a residual disinfectant resulted in lower viral taxonomic diversity and metabolic potential. Additionally, drinking water viruses carry antibiotic resistance genes and genes for survival in stressful conditions. These findings highlight the diversity of viral communities in drinking water systems and the potential impact on water quality.
Article
Microbiology
Naveen Kachroo, Dirk Lange, Kristina L. Penniston, Joshua Stern, Gregory Tasian, Petar Bajic, Alan J. Wolfe, Mangesh Suryavanshi, Andrea Ticinesi, Tiziana Meschi, Manoj Monga, Aaron W. Miller
Summary: This research investigated whether questions related to the urinary or gut microbiome and urinary stone disease (USD) can be answered through metagenome-wide association studies (MWAS). The study found significant differences in microbiome composition based on factors like USD status, stone composition, age group, and study location. Results indicate the importance of standardizing experimental protocols in the field to assess microbiome differences accurately.
Article
Microbiology
Taylor J. Busby, Craig R. Miller, Nancy A. Moran, James T. Van Leuven
Summary: Microbial communities in animal digestive systems play crucial roles in host development and health. However, little is known about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. This study focuses on bacteriophages in the gut of honey bees and reveals their conservation and specialization in different geographic locations.
Article
Psychiatry
Mohammad Tahseen Al Bataineh, Axel Kuenstner, Nihar Ranjan Dash, Rushud Mahmood Abdulsalam, Rafla Zaid Ali Al-Kayyali, M. Besher Adi, Habiba S. Alsafar, Hauke Busch, Saleh Mohamed Ibrahim
Summary: Alterations in the oral microbiota composition may influence the mental health of cigarette smokers. This study found that smokers in the avoidance group had a higher richness and diversity of the oral microbiome. Significant differences in abundance were observed in certain phyla between the avoidance and activation groups. Network analysis identified different hub nodes in each group. Furthermore, functional analysis revealed enrichment of a specific pathway in the avoidance group. These findings provide evidence for depression-related changes in the oral microbiota and their potential impact on mental health.
FRONTIERS IN PSYCHIATRY
(2022)
Article
Microbiology
Ignacio Montero, Desiree Barrientos, Claudio Hidalgo-Cantabrana, Noelia Martinez-Alvarez
Summary: GutAlive (R) is a unique stool collection kit that generates an anaerobic atmosphere, preserving the original microbiome composition and diversity. It shows superior performance in maintaining bacterial viability and DNA integrity over time, making it suitable for fecal microbiome analysis.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Cell Biology
Heloise Tudela, Sandrine P. Claus, Maya Saleh
Summary: The gut microbiota, a diverse community of microorganisms in the gastrointestinal tract, has a significant impact on health and disease. Keystone species, essential microbes for microbiota balance, play crucial roles in maintaining essential functions and their identification is crucial for the development of microbiome-based therapeutics. Understanding the functions of keystone species is a major step towards comprehending microbiome dynamics in disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Plant Sciences
Ping Kong, Xiaoping Li, Melissa Sharifi, Adria Bordas, Chuanxue Hong
Summary: Differential tolerance of English boxwood to boxwood blight is associated with the dominance of bacteria over fungi in the leaf tissue. Our study also suggests that the resistance of English boxwood to blight is attributed to bacteria dominance and a healthier community network.
PHYTOBIOMES JOURNAL
(2023)
Article
Plant Sciences
Ping Kong, Xiaoping Li, Melissa Sharifi, Adria Bordas, Chuanxue Hong
Summary: The tolerance of English boxwood to boxwood blight is associated with the ratio of bacteria and fungi in the leaf tissue. Tolerant plants have a higher abundance of bacteria and lower abundance of fungi compared to susceptible plants. Network analysis shows that the tolerant community has a simpler and healthier network structure. Therefore, the resistance of English boxwood to blight is likely attributed to the dominance of bacteria and a synergic community network.
PHYTOBIOMES JOURNAL
(2023)
Article
Plant Sciences
Shyam L. Kandel, Peter M. Henry, Polly H. Goldman, Beiquan Mou, Steven J. Klostermant
Summary: This study characterized the structure and function of spinach seed microbiomes, revealing that they are highly influenced by geographic origin and pathogen infestation. Even in noninfested seeds, potential beneficial bacteria and plant pathogens were found. This research provides an important first step in identifying spinach seedborne microorganisms that could improve plant health and inadvertently carried plant pathogens to new locations.
PHYTOBIOMES JOURNAL
(2022)
Article
Microbiology
Victoria Pascal Andreu, Hannah E. Augustijn, Koen van den Berg, Justin J. J. van der Hooft, Michael A. Fischbach, Marnix H. Medema
Summary: Microbial gene clusters encoding biosynthesis of metabolites are crucial for microbial ecosystems. BiG-MAP is a bioinformatic tool that profiles gene cluster abundance and expression levels in microbiome samples, allowing for hypothesis generation on functional roles and associations with phenotypes of interest.
Article
Biotechnology & Applied Microbiology
Stephanie P. Gill, William R. Hunter, Laura E. Coulson, Ibrahim M. Banat, Jakob Schelker
Summary: This study investigated the effects of chemical and biological surfactants on freshwater biofilms and found that both types of surfactants significantly reduced microbial diversity and affected biofilm metabolism, as evidenced by changes in extracellular enzyme activities.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Clarisse Marotz, Kellen J. Cavagnero, Se Jin Song, Daniel McDonald, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, Edgar Diaz, Rob Knight
Summary: This study reanalyzed data from a large sample storage study, confirming that 95% ethanol is an effective, practical, and cost-effective preservative that can preserve samples at room temperature for weeks. It also identified the optimal ratio of 95% ethanol to sample in stool and saliva samples, providing a solution that enables crowdsourcing microbiome studies and lowers the barrier for collecting diverse samples.
Article
Engineering, Environmental
Changcai Wu, Zhinan Wang, Yan Ma, Junyu Luo, Xueke Gao, Jun Ning, Xiangdong Mei, Dongmei She
Summary: This study investigated the effects of the neonicotinoid insecticide thiamethoxam on bacterial communities and metabolic functions in two types of soils. Thiamethoxam treatment significantly affected soil bacterial abundance, reduced microbial diversity, and temporarily altered the bacterial community structure. The study also identified changes in the populations of certain beneficial and pollutant-degrading bacteria, as well as the increased abundance of biodegradation and pesticide degradation genes, including cytochrome P450. The conclusions of this study will contribute to safety evaluations and degradation-related research on neonicotinoid insecticides in soil.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Microbiology
Zhiguo Zhang, Lu Zhang, Guoqing Zhang, Ze Zhao, Hui Wang, Feng Ju
Summary: Duplicate reads from metagenomic sequencing libraries have impacts on metagenomic assembly and binning. This study investigated their effects on metagenomes with distinct microbiome complexities, revealing that deduplication significantly increased binning yields and reduced computational costs. Therefore, the removal of duplicate reads should be recommended in high complexity metagenomes before analysis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Physiology
Quanhua Liu, Geoffrey W. Abbott, Jiaxue Li, Ting Liu, Qifeng Wang, Feng Ju, Zhaoyang Hu
Summary: Testicular torsion is a urological emergency that requires immediate surgery, but detorsion can lead to testicular tissue damage. This study investigated whether testicular torsion/detorsion affects myocardial function and examined the potential cardioprotective effect of remote ischemic post-conditioning (RIPost). The results showed that testicular torsion/detorsion led to impaired cardiac function and increased serum markers of cardiac injury. However, RIPost attenuated the remote cardiac dysfunction induced by testicular torsion/detorsion and enhanced the phosphorylation of ventricular STAT-3, a key component of the SAFE signaling pathway. These findings suggest that testicular torsion/detorsion can cause cardiac dysfunction, but RIPost may protect against it through the activation of STAT-3 signaling.
AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY, INTEGRATIVE AND COMPARATIVE PHYSIOLOGY
(2023)
Article
Environmental Sciences
Hui Wang, Limin Lin, Lu Zhang, Ping Han, Feng Ju
Summary: This study investigates the effect of the nitrification inhibitor allylthiourea (ATU) on the microbiome assembly and functional potential in enhanced biological phosphorus removal (EBPR) systems. The results showed that ATU increased microbiota structural similarity and compositional convergence, and enhanced determinism in the assembly of EBPR microbiome. Additionally, ATU promoted the enrichment of functional genes involved in phosphate transport and polyphosphate synthesis and degradation.
ENVIRONMENTAL RESEARCH
(2023)
Article
Engineering, Environmental
Yaqi Guo, Chenchen Wang, Panpan Huang, Jing Li, Chunsheng Qiu, Yaohui Bai, Chaocan Li, Jingjie Yu
Summary: A dynamic multimedia fate model of chemicals with spatial differentiation was constructed to describe the spatio-temporal distribution of chemicals in flowing lake systems. The model, coupling the level IV fugacity model with lake hydrodynamics, was successfully applied to study the distribution of four phthalates (PAEs) in a lake recharged by reclaimed water. The results showed significant spatial heterogeneity in the distributions of PAEs in both lake water and sediment, which was explained by the analysis of PAE transfer fluxes. The model can provide important information and accurate data support for the scientific management of chemicals in flowing lake systems.
Article
Endocrinology & Metabolism
Linan Ren, Yao Wang, Feng Ju, Meixin Sun, Xiaokun Gang, Guixia Wang
Summary: This study used bidirectional Mendelian randomization to investigate the causal relationship between sarcopenia and diabetic nephropathy (DN). The results suggest that a decrease in appendicular lean mass increases the risk of developing DN, while DN progression is associated with reduced grip strength. However, there is no overall causal relationship between sarcopenia and DN.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Multidisciplinary Sciences
Suyan Gao, Zhaolin Du, Feng Ju, Peisheng Yan, Ben Niu, Yanpo Yao
Summary: The yield and quality of maize are affected by environmental factors and rhizosphere microorganisms, especially mycotoxin pollution. A study found that bacteria in high aflatoxin contamination areas were significantly correlated with aflatoxin contamination of maize. These findings will support strategies to improve maize yield and contamination control.
Article
Environmental Sciences
Kaiyang Jiang, Hongna Li, Wen Liu, Yi Jiang, Zhiguo Zhang, Feng Ju, Tingting Song, Binxu Li, Xuerong Wang, Changxiong Zhu
Summary: Electrochemical disinfection (ED) effectively removes antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in wastewater treatment. This study investigated the disinfection mechanism at a microcosmic level using different strains of Escherichia coli (E. coli) with varying antibiotic resistant phenotypes. Findings showed that bacteria with multiple antibiotic resistance had higher viability during disinfection compared to those with fewer resistance. Notably, antibiotic-resistant phenotypes remained largely unchanged during disinfection, while genotypes closely responded to E. coli's resistance. β-lactamase resistance genes played a significant role in cross-resistance between antibiotics and electrochemical oxidation by strengthening the cell wall and membrane. This study provides important insights into and control of antibiotic resistance with advanced oxidation processes.
Article
Engineering, Environmental
Xinyu Zhu, Songmei Zhu, Ze Zhao, Xiaoxi Kang, Feng Ju
Summary: Anaerobic digestion of food waste and potential co-digestion with biodegradable packaging material are effective strategies for resource recovery. Understanding the microbiome dynamics and genetic potential for hydrolysis is important for process control and optimization. This study found that the microbiome composition and activity-dormancy status changed during digestion, with certain microbes showing high abundance but entering dormancy after substrate consumption and others showing low abundance but high activity. In addition, adding polylactic acid (PLA) to the digestion process enhanced methane production without significant changes in microbiome composition. These findings provide a theoretical basis for efficient co-digestion processes and microbiome management.
CHEMICAL ENGINEERING JOURNAL
(2023)
Review
Immunology
Feng Ju, Dawei Wang, Lan Huang, Chun Jiang, Ce Gao, Cunquan Xiong, Guanghua Zhai
Summary: Primary liver cancer, mostly hepatocellular carcinoma, is highly prevalent in China. Liver transplantation offers new hope to patients, but immunosuppression increases the risk of HCC recurrence and metastasis. Blocking the PD-1/PD-L1 signaling pathway shows promise in tumor immunotherapy for liver cancer patients, but its application in transplantation patients is still controversial.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Limin Lin, Feng Ju
Summary: This study evaluated the suitability of different 16S rRNA gene primers and reference databases for microbiota profiling. The results showed that MiDAS 4.8 database and V4 region are recommended for best simultaneous analysis of bacterial and archaeal community diversity and structure.
Article
Green & Sustainable Science & Technology
Bob Adyari, Liyuan Hou, Lanping Zhang, Nengwang Chen, Feng Ju, Longji Zhu, Chang-Ping Yu, Anyi Hu
Summary: In this study, the profiles of antibiotic resistance genes (ARGs) in particle-attached (PA) and free-living (FL) lifestyles were examined in the Shuikou Reservoir, Southern China. The results showed that seasonal hydrological dynamics played a critical role in shaping ARGs in PA and FL and in the transition of ARGs between the two lifestyles. Horizontal gene transfer was found to influence ARG profiles in both PA and FL, while they responded differently to the physicochemical changes under seasonal hydrological dynamics. The study also identified both non-conservative and conservative ARGs associated with PA and FL lifestyles.
ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY
(2023)
Article
Green & Sustainable Science & Technology
Bob Adyari, Liyuan Hou, Lanping Zhang, Nengwang Chen, Feng Ju, Longji Zhu, Chang-Ping Yu, Anyi Hu
Summary: This study investigated the dynamics of antibiotic resistance genes (ARGs) in deep freshwater reservoirs in Southern China, focusing on the particle-attached (PA) and free-living (FL) lifestyles. The results showed that seasonal hydrological dynamics played a critical role in influencing the ARGs in PA and FL, as well as the transition of ARGs between the two lifestyles. ARCs in both PA and FL were shaped by horizontal gene transfer and exhibited distinct responses to physicochemical changes under seasonal hydrological dynamics. The study provided valuable insights into the lifestyle of ARGs and the impact of seasonal hydrological changes in a deep freshwater ecosystem.
ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY
(2023)
Article
Engineering, Environmental
Donglin Wang, Jiayu Shang, Hui Lin, Jinsong Liang, Chenchen Wang, Yanni Sun, Yaohui Bai, Jiuhui Qu
Summary: This study develops a bio-informatic pipeline using deep learning techniques to identify phages carrying antibiotic resistance genes (ARGs) and predict their hosts, with a focus on pathogens. The study discovers that temperate phages in a landscape lake replenished by reclaimed water predominantly carry ARGs related to multidrug resistance and beta-lactam antibiotics. In silico analysis and qPCR confirm a positive correlation between temperate phages and host pathogens, and seasonal variations in the abundance of phages and chromosomes carrying ARGs.
Article
Biotechnology & Applied Microbiology
Hui Lin, Xue Ning, Donglin Wang, Qiaojuan Wang, Yaohui Bai, Jiuhui Qu
Summary: This study reveals a previously unknown mechanism for the hormetic effect of low-dose sulfonyl-containing compounds in stimulating cell proliferation. It provides critical insights into the health and ecological effects of antibiotics.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Xinyu Zhu, Ping Li, Feng Ju
Summary: Biowaste fermentation is a promising technology for low-carbon print bioenergy and biochemical production. This study investigated the microbiome dynamics and fermentation product profiles of biowaste fermentation, uncovering the mechanisms of microbiome activity dynamics shaping the biowaste fermentation product profiles. These findings provide a fundamental basis for the development of microbiome-guided engineering approaches to modulate biowaste fermentation toward high-value product recovery.
ENGINEERING IN LIFE SCIENCES
(2023)
