Article
Food Science & Technology
Yu Xia, Min Zhu, Yake Du, Zhengyun Wu, Katsuya Gomi, Wenxue Zhang
Summary: This study investigated the proteins associated with the activity of saccharifying enzymes in daqu by comparing the protein composition between two types of daqu. It was found that the amylase system and cellulase system were the main saccharifying enzymes, with different genera contributing to each system. Additionally, the up-regulated amylase proteins in jiangxiangxing daqu were mainly from Aspergillus, Rhizomucor, Byssochlamys, and Thermomyces, while the cellulase system was mainly contributed by Thermoascus. These findings provide insights for improving saccharification efficiency in Baijiu production.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Food Science & Technology
Wenzhi Lv, Feng Li, Changan Li
Summary: Inoculated fermentation is widely used to improve food production, but the influence of multi-species starters on food fermentation is still unclear. This study compared the effects of different types of Daqu on liquor fermentation, with/without the inoculation of Bacillus licheniformis. The inoculated Daqu had a higher abundance of Bacillus and lower abundance of Lactobacillus compared to the non-inoculated Daqu. Metatranscriptomic analysis revealed that Kazachstania, Naumovozyma, Saccharomyces, Nakaseomyces, and Lactobacillus were active during liquor fermentation, and their transcription patterns were influenced by the inoculated Daqu. The results suggested that using inoculated Daqu could enhance the production of ethanol, acetic acid, and lactic acid in liquor fermentation.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Food Science & Technology
Ahmad Ud Din, Waqar Ahmad, Taj Malook Khan, Jun Wang, Jianbo Wu
Summary: This study aimed to characterize the microbial ecosystem of Zaopei Baijiu Daqu (ZBD) starter cultures for specific microbes with probiotic properties. The results revealed abundant beneficial microbes in the starter culture, opening up possibilities for further in-depth analysis and evaluation of their valuable roles in in vitro and in vivo studies.
Article
Food Science & Technology
Mengmeng Lu, Weicheng Zhou, Fang Ji, Jianfeng Wu, Yao Nie, Cong Ren, Yan Xu
Summary: The enrichment approach using oligotrophic culturing successfully cultivated the pit mud microbiota, enriching Euryarchaeota, Bacteroidetes, and Firmicutes as the top 3 phyla. Methanogens and bacteria were both enriched, with 31 genera successfully enriched, including 11 dominant genera in pit mud and 20 rare genera. Metagenomic sequencing revealed the dominance of Aceticlastic Methanosaeta and Methanosarcina in the enriched consortia, and the importance of nutrients in sustaining methanogenesis.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2021)
Article
Horticulture
Hongfei Li, Fang Song, Xiaoxiao Wu, Chongling Deng, Qiang Xu, Shu'ang Peng, Zhiyong Pan
Summary: The study identified significant changes in rhizosphere and root bacterial genera in response to CLas infection, with particular impacts on carbohydrate metabolism and phosphoinositide signaling pathways.
Article
Biotechnology & Applied Microbiology
Yijuan Han, Dongyan Shao, Cuicui Han, Qingsheng Huang, Wen Zhao
Summary: The present study used 16S rRNA gene sequencing to investigate the impact of microgravity on human gut microbiota in vitro. The results showed that microgravity significantly altered the richness and diversity of the microbiota. Certain bacteria related to anti-inflammatory effects decreased in abundance, while others increased. Microgravity also affected the metabolism of the gut microbiota. These findings suggest that exposure to a microgravity environment can disrupt the gut microbiota.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Food Science & Technology
Shibo Ban, Lingna Chen, Shuangxue Fu, Qun Wu, Yan Xu
Summary: This study reveals the effects of processing parameters on the core microbiota in spontaneous fermentation of Chinese liquor starter. The fermentation moisture and temperature were found to significantly affect the core microbiota. Furthermore, room humidity and room temperature were identified as influencing factors for the processing parameters, and models were constructed to predict the population of core microbiota based on these factors.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Monika Mioduchowska, Bartosz Nitkiewicz, Milena Roszkowska, Uros Kacarevic, Piotr Madanecki, Tom Pinceel, Tadeusz Namiotko, Bartlomiej Goldyn, Lukasz Kaczmarek
Summary: High-throughput sequencing revealed Wolbachia infection in tardigrade species, with the bacteria found in adult specimens. Meanwhile, Rickettsiales bacteria were detected in both eutardigrade eggs and adult specimens. The discovery of Wolbachia in tardigrades opens up new research avenues to explore the specifics of this interaction.
Article
Food Science & Technology
Yang Yang, Song-Tao Wang, Zhen-Ming Lu, Xiao-Juan Zhang, Li-Juan Chai, Cai-Hong Shen, Jin-Song Shi, Zheng-Hong Xu
Summary: This study investigates the microbial metabolic network of daqu during fermentation and reveals the different metabolic roles of microorganisms, highlighting the formation mechanism of daqu's aromas and enzymes. The study shows the potential predominant populations responsible for flavor development in daqu and identifies specific microorganisms involved in key flavor pathways and metabolisms.
FOOD RESEARCH INTERNATIONAL
(2021)
Review
Microbiology
Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, Andre Karch, Nicole Ruebsamen
Summary: Reproducibility in microbiome studies is hindered by a lack of consensus on data analysis strategies. The complex nature of microbiome data, combined with increasingly sophisticated research questions, requires more advanced analytical methods. Current analysis strategies in microbiome studies show significant heterogeneity, particularly in differential abundance testing, indicating a need for better guidance in analyzing increasingly complex research questions.
Article
Food Science & Technology
Rei Peraza, Gabriel G. Perron
Summary: The influence of microbial diversity on flavor profile in fermented foods is known as microbial terroir. The study found that fermentation is primarily influenced by the main ingredient being cooked and that different fermented food groups harbor similar microbial communities. This research helps us understand the value of local fermented food in our culinary journey.
INTERNATIONAL JOURNAL OF GASTRONOMY AND FOOD SCIENCE
(2022)
Article
Food Science & Technology
Yufang Liu, Junna Cai, Fuxin Zhang
Summary: The study found that different types of milk have different effects on the intestinal microbiota of mice. Significant differences in nutrient components between breast milk, cow milk, and goat milk can alter the composition and functional features of the intestinal microbiota. The protein, minerals, and amino acid content of milk are correlated with specific bacterial groups in the intestinal microbiota.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ryan B. Ghannam, Stephen M. Techtmann
Summary: Advances in nucleic acid sequencing technology have expanded our understanding of microbial diversity. Machine learning is a valuable tool for analyzing microbial community data and making predictions, but the interpretability of the models must be considered.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Immunology
Hadar Mudrik-Zohar, Shaqed Carasso, Tal Gefen, Anat Zalmanovich, Michal Katzir, Yael Cohen, Yossi Paitan, Naama Geva-Zatorsky, Michal Chowers
Summary: Sequencing tools uncover the complex biodiversity of IDFU and highlight the high prevalence of anaerobes and Gram-negative bacteria in these ulcers. Furthermore, sequencing results reveal possible associations among certain genera, species, and bacterial functional genes to clinical outcomes.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Jongoh Shin, Jung-Ran Noh, Donghui Choe, Namil Lee, Yoseb Song, Suhyung Cho, Eun-Jung Kang, Min-Jeong Go, Seok Kyun Ha, Dong-Ho Chang, Jae-Hoon Kim, Yong-Hoon Kim, Kyoung-Shim Kim, Haiyoung Jung, Myung Hee Kim, Bong-Hyun Sung, Seung-Goo Lee, Dae-Hee Lee, Byoung-Chan Kim, Chul-Ho Lee, Byung-Kwan Cho
Summary: The study revealed changes in gut microbial communities and functions during aging in mouse models, showing that rejuvenation procedures can restore the microbiota and intestinal immunity of aged mice to levels comparable to young mice. Oral administration of Akkermansia extended the health span of aged mice, indicating its potential for therapeutic strategies to achieve healthy active aging.
Article
Biochemistry & Molecular Biology
Kaimeng Wang, Caiyao Zhao, Sunhuan Xiang, Kunyu Duan, Xiaoli Chen, Xing Guo, Sunil Kumar Sahu
Summary: Recently, a new nuclei isolation approach, called FACS-free single-nucleus RNA sequencing (snRNA-seq), was developed to overcome the limitations of scRNA-seq in plants. This study validated the robustness of snRNA-seq methodology in mature Arabidopsis plant tissue and demonstrated its high quality data and utility in cell type classification and marker gene identification. The advantages of snRNA-seq, such as the ability to use frozen samples and reduced biased cellular coverage and transcriptional artifacts, were also highlighted.
Article
Multidisciplinary Sciences
Xing Guo, Fang Wang, Dongming Fang, Qiongqiong Lin, Sunil Kumar Sahu, Liuming Luo, Jiani Li, Yewen Chen, Shanshan Dong, Sisi Chen, Yang Liu, Shixiao Luo, Yalong Guo, Huan Liu
Summary: In this study, the authors assemble the genome of Acorus gramineus, a wetland plant, and find that it has fewer genes compared to most other monocots. They also confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of whole-genome duplication observed in the majority of monocot clades. Furthermore, they identify gene contractions and expansions related to plant architecture, stress resistance, light harvesting, and essential oil metabolism.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Jianmu Su, Yayu Wang, Mei Bai, Tianhua Peng, Huisi Li, Hui-Juan Xu, Guifang Guo, Haiyi Bai, Ning Rong, Sunil Kumar Sahu, Hanjun He, Xiangxiu Liang, Canzhi Jin, Wei Liu, Mikael Lenz Strube, Lone Gram, Yongtao Li, Ertao Wang, Huan Liu, Hong Wu
Summary: This study used a multi-omics approach to investigate the effects of environmental factors on the accumulation of monoterpenes in citrus peel. It was found that soil nutrients and root-associated microbiome play important roles in the production of monoterpenes. The soil environment, including high salinity and certain nutrients, can enhance monoterpene content in citrus peel by promoting the expression of specific genes. Additionally, interactions between rhizosphere microorganisms and the host immune system can activate terpene synthesis and contribute to monoterpene accumulation.
Article
Ecology
Marty Kardos, Yaolei Zhang, Kim M. Parsons, A. Yunga, Hui Kang, Xun Xu, Xin Liu, Craig O. Matkin, Peijun Zhang, Eric J. Ward, M. Bradley Hanson, Candice Emmons, Michael J. Ford, Guangyi Fan, Songhai Li
Summary: Understanding the factors that cause endangered populations to either grow or decline is crucial for preserving biodiversity. Conservation efforts often focus on extrinsic threats but neglect the genetic factors that can affect population dynamics. This study shows that inbreeding depression strongly influences the population dynamics of an endangered killer whale population, and that conservation efforts need to consider these genetic factors.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Plant Sciences
Jin Xu, Yayu Wang, Yunzeng Zhang, Nadia Riera, Jinyun Li, Kelley J. Clark, Tao Jin, Hongyun Chen, Jiawen Wen, Wenbo Ma, Huan Liu, Nian Wang
Summary: In this study, we investigated the genetic traits underlying the citrus microbiome by sequencing the metagenome of leaf, root, and rhizosphere soil samples, as well as the genome of corresponding citrus genotypes. Through genome-wide association study (GWAS) analysis, we found significant associations between citrus genes and specific genera and functional traits of the microbiome. We also discovered the importance of bacterial secretion systems, mobility-related genes, chemotaxis, and flagella genes for bacteria colonization in leaf and root tissues. Additionally, microbiome-associated host genes were mainly involved in plant immunity, transporters, hormones, and metabolism. This study provides valuable information for utilizing genotypes and beneficial bacteria in microbiome engineering and gene editing to improve the host microbiota.
PHYTOBIOMES JOURNAL
(2023)
Article
Multidisciplinary Sciences
Boyang Cao, Huijuan Luo, Nannan Li, Kang Shao, Kui Wu, Sunil Kumar Sahu, Fuqiang Li, Cong Lin
Summary: In this study, we developed two WGBS library construction methods optimized for the DNBSEQ-Tx sequencer. The data sequenced on the DNBSEQ-Tx platform met the quality controls required for WGBS, and closely resembled the coverage shown by the data generated by the Illumina platform. Therefore, we conclude that DNBSEQ-Tx can be used for a wide range of WGBS research.
Article
Plant Sciences
Sunil Kumar Sahu, Min Liu, Ruirui Li, Yewen Chen, Guanlong Wang, Dongming Fang, Durgesh Nandini Sahu, Jinpu Wei, Sibo Wang, Huan Liu, Chengzhong He
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Sunil Kumar Sahu, Min Liu, Yewen Chen, Jinshan Gui, Dongming Fang, Xiaoli Chen, Ting Yang, Chengzhong He, Le Cheng, Jinlong Yang, Durgesh Nandini Sahu, Linzhou Li, Hongli Wang, Weixue Mu, Jinpu Wei, Jie Liu, Yuxian Zhao, Shouzhou Zhang, Michael Lisby, Xin Liu, Xun Xu, Laigeng Li, Sibo Wang, Huan Liu
Summary: Wood is an important and renewable source of energy, but there are still many aspects of its formation that have not been studied. In this study, chromosome-scale genome assemblies of three timber trees were performed, providing valuable genetic resources for comparative genomic analyses and a better understanding of wood properties in non-model woody species.
Article
Multidisciplinary Sciences
Xiumei Lin, Xueqian Yang, Chuan Chen, Wen Ma, Yiqi Wang, Xuerong Li, Kaichen Zhao, Qiuting Deng, Weimin Feng, Yuting Ma, Hui Wang, Lveming Zhu, Sunil Kumar Sahu, Fengzhen Chen, Xiuqing Zhang, Zhiqiang Dong, Chuanyu Liu, Longqi Liu, Chang Liu
Summary: By using single-nucleus ATAC-seq technique, we generated a chromatin accessibility dataset for the first day (3.3 hpf, 5.25 hpf, 6 hpf, 10 hpf, 12 hpf, 18 hpf, and 24 hpf) of zebrafish embryogenesis, obtaining 51,620 high-quality nuclei and 23 clusters. By integrating snATAC-seq data with single-cell RNA-seq data, we described the dynamics of chromatin accessibility and gene expression across developmental time points, validating the accuracy of the chromatin landscape data. Our data serves as a valuable resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.
Article
Genetics & Heredity
Guohai Hu, Yue Wang, Christopher Blake, Mathilde Nordgaard, Xin Liu, Bo Wang, Akos T. Kovacs
Summary: This study used experimental evolution and whole-genome sequencing to analyze the evolutionary adaptation of B. subtilis on different plant species and in alternating host plant regimes. The results showed parallel evolution across different biological levels, with the genetic level exhibiting the greatest adaptation in heterogeneous and spatially structured environments. Species-specific adaptation and a trade-off between motility and biofilm development were also observed. Additionally, condition-specific and common targeted genes were identified in different biofilm adaptation settings. These findings provide insights into the evolutionary patterns and genetic mechanisms of B. subtilis in the plant rhizosphere, and can contribute to strain improvements for sustainable agriculture.
MICROBIAL GENOMICS
(2023)
Review
Biochemistry & Molecular Biology
Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj Jaiswal
Summary: The development of pan-genomics enables the identification and introduction of lost genes and alleles in crops, which can improve crop yield and resistance. This offers new avenues for targeted breeding and helps mitigate the impact of global climate change.
Article
Plant Sciences
Dan Zong, Huan Liu, Peihua Gan, Shaojie Ma, Hongping Liang, Jinde Yu, Peilin Li, Tao Jiang, Sunil Kumar Sahu, Qingqing Yang, Deguo Zhang, Laigeng Li, Xu Qiu, Wenwen Shao, Jinlong Yang, Yonghe Li, Xuanmin Guang, Chengzhong He
Summary: This study provides valuable insights into the genome evolution and molecular basis of the high concentration of ascorbate in Rosa roxburghii and Rosa sterilis.
Article
Plant Sciences
Xiaoen Huang, Hongge Jia, Jin Xu, Yuanchun Wang, Jiawen Wen, Nian Wang
Summary: This study achieved transgene-free plant genome editing in the T0 generation using a co-editing strategy. The researchers successfully edited the ALS gene and gene(s) of interest, and obtained transgene-free mutants using appropriate selection markers and screening methods. This strategy is particularly useful for vegetatively propagated and perennial plant species.
