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Article ; Online: Advances and challenges in cataloging the human gut virome.

Li, Junhua / Yang, Fangming / Xiao, Minfeng / Li, Aixin

2022 Volume 30, Issue 7, Page(s) 908–916

Abstract: The human gut virome, which is often referred to as the "dark matter" of the gut microbiome, remains understudied. A better understanding of the composition and variations of the gut virome across populations is critical for exploring its impact on ... ...

Abstract	The human gut virome, which is often referred to as the "dark matter" of the gut microbiome, remains understudied. A better understanding of the composition and variations of the gut virome across populations is critical for exploring its impact on diseases and health. A series of advances in the characterization of human gut virome have unveiled high genetic diversity and various functional potentials of gut viruses. Here, we summarize the recently available human gut virome databases and discuss their features, procedures, and challenges with the intention to provide a reference to researchers to use while choosing a profiling database. We also propose a "best practice" for cataloging the viral population.
MeSH term(s)	Bacteriophages/genetics ; Cataloging ; Gastrointestinal Microbiome/genetics ; Humans ; Virome/genetics ; Viruses/genetics
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2022.06.003
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Article ; Online: Re: Mikkel Fode, Christian Fuglesang S. Jensen, Peter B. Østergren. How Should the Medical Community Respond to the Low Quality of Medical Information on Social Media? Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.09.050.

Zu, Xiongbing / Chen, Minfeng / Guan, Xiao

European urology open science

2021 Volume 24, Page(s) 9–10

Language	English
Publishing date	2021-01-04
Publishing country	Netherlands
Document type	Journal Article
ISSN	2666-1683
ISSN (online)	2666-1683
DOI	10.1016/j.euros.2020.12.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Jonathan H Bethke / Helena R Ma / Ryan Tsoi / Li Cheng / Minfeng Xiao / Lingchong You

Molecular Systems Biology, Vol 19, Iss 2, Pp n/a-n/a (2023)

2023

Abstract: Abstract Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid ... ...

Abstract	Abstract Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation‐growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.
Keywords	conjugation ; fitness ; plasmid ; resistance ; tradeoff ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: PhaGAA: an integrated web server platform for phage genome annotation and analysis.

Wu, Jiawei / Liu, Qingrui / Li, Min / Xu, Jiliang / Wang, Chen / Zhang, Junyin / Xiao, Minfeng / Bin, Yannan / Xia, Junfeng

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 3

Abstract: Motivation: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. ...

Abstract	Motivation: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed. Results: Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate the prophage genome at DNA and protein levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists and help advance the phage synthetic biology in basic and application research. Availability and implementation: PhaGAA is freely available at http://phage.xialab.info/.
MeSH term(s)	Bacteriophages/genetics ; Software ; Computers ; Metagenome ; Genome, Bacterial ; Molecular Sequence Annotation
Language	English
Publishing date	2023-03-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad120
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Article ; Online: Vertical and horizontal gene transfer tradeoffs direct plasmid fitness.

Bethke, Jonathan H / Ma, Helena R / Tsoi, Ryan / Cheng, Li / Xiao, Minfeng / You, Lingchong

Molecular systems biology

2022 Volume 19, Issue 2, Page(s) e11300

Abstract: Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and ... ...

Abstract	Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.
MeSH term(s)	Gene Transfer, Horizontal ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-12-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2193510-5
ISSN	1744-4292 ; 1744-4292
ISSN (online)	1744-4292
ISSN	1744-4292
DOI	10.15252/msb.202211300
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Article ; Online: Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism.

Ma, Lijia / Deng, Wenwei / Bai, Yuan / Du, Zhanwei / Xiao, Minfeng / Wang, Lin / Li, Jianqiang / Nandi, Asoke K

IEEE/ACM transactions on computational biology and bioinformatics

2023 Volume 20, Issue 6, Page(s) 3772–3785

Abstract: Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in ... ...

Abstract	Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in recent years. Metagenomics sequencing technique can sequence microbial communities directly from an environmental sample. Identifying phage sequences from metagenomic data is a vital step in the downstream of phage analysis. However, the existing methods for phage identification suffer from some limitations in the utilization of the phage feature for prediction, and therefore their prediction performance still need to be improved further. In this article, we propose a novel deep neural network (called MetaPhaPred) for identifying phages from metagenomic data. In MetaPhaPred, we first use a word embedding technique to encode the metagenomic sequences into word vectors, extracting the latent feature vectors of DNA words. Then, we design a deep neural network with a convolutional neural network (CNN) to capture the feature maps in sequences, and with a bi-directional long short-term memory network (Bi-LSTM) to capture the long-term dependencies between features from both forward and backward directions. The feature map consists of a set of feature patterns, each of which is the weighted feature extracted by a convolution filter with convolution kernels in the CNN slide along the input feature vectors. Next, an attention mechanism is used to enhance contributions of important features. Experimental results on both simulated and real metagenomic data with different lengths demonstrate the superiority of the proposed MetaPhaPred over the state-of-the-art methods in identifying phage sequences.
MeSH term(s)	Bacteriophages/genetics ; Neural Networks, Computer ; Algorithms ; Metagenome/genetics ; Microbiota
Language	English
Publishing date	2023-12-25
Publishing country	United States
Document type	Journal Article
ISSN	1557-9964
ISSN (online)	1557-9964
DOI	10.1109/TCBB.2023.3322870
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning.

Wang, Chen / Zhang, Junyin / Cheng, Li / Wu, Jiawei / Xiao, Minfeng / Xia, Junfeng / Bin, Yannan

IEEE journal of biomedical and health informatics

2022 Volume 26, Issue 10, Page(s) 5258–5266

Abstract: With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of data ... ...

Abstract	With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of data makes it possible to establish computational models for promoter identification with robustness. In this work, we introduce DPProm, a two-layer model composed of DPProm-1L and DPProm-2L, to predict promoters and their types for phages. On the first layer, as a dual-channel deep neural network ensemble method fusing multi-view features (sequence feature and handcrafted feature), the model DPProm-1L is proposed to identify whether a DNA sequence is a promoter or non-promoter. The sequence feature is extracted with convolutional neural network (CNN). And the handcrafted feature is the combination of free energy, GC content, cumulative skew, and Z curve features. On the second layer, DPProm-2L based on CNN is trained to predict the promoters' types (host or phage). For the realization of prediction on the whole genomes, the model DPProm, combines with a novel sequence data processing workflow, which contains sliding window and merging sequences modules. Experimental results show that DPProm outperforms the state-of-the-art methods, and decreases the false positive rate effectively on whole genome prediction. Furthermore, we provide a user-friendly web at http://bioinfo.ahu.edu.cn/DPProm. We expect that DPProm can serve as a useful tool for identification of promoters and their types.
MeSH term(s)	Bacteriophages/genetics ; DNA ; Deep Learning ; Genomics/methods ; Humans ; Promoter Regions, Genetic/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2695320-1
ISSN	2168-2208 ; 2168-2194
ISSN (online)	2168-2208
ISSN	2168-2194
DOI	10.1109/JBHI.2022.3193224
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Zs.A 5483: Show issues

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Article ; Online: Characterization of a novel genus of jumbo phages and their application in wastewater treatment.

Hu, Ming / Xing, Bo / Yang, Minghua / Han, Rui / Pan, Huazheng / Guo, Hui / Liu, Zhen / Huang, Tao / Du, Kang / Jiang, Shangyi / Zhang, Qian / Lu, Wenjing / Huang, Xun / Zhou, Congzhao / Li, Junhua / Song, Wenchen / Deng, Ziqing / Xiao, Minfeng

iScience

2023 Volume 26, Issue 6, Page(s) 106947

Abstract: Phages widely exist in numerous environments from wastewater to deep ocean, representing a huge virus diversity, yet remain poorly characterized. Among them, jumbo phages are of particular interests due to their large genome (>200 kb) and unusual biology. ...

Abstract	Phages widely exist in numerous environments from wastewater to deep ocean, representing a huge virus diversity, yet remain poorly characterized. Among them, jumbo phages are of particular interests due to their large genome (>200 kb) and unusual biology. To date, only six strains of jumbo phages infecting
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.106947
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Investigation on Geometry Computation of Spaceborne GNSS-R Altimetry over Topography

Minfeng Song / Xiufeng He / Milad Asgarimehr / Weiqiang Li / Ruya Xiao / Dongzhen Jia / Xiaolei Wang / Jens Wickert

Remote Sensing, Vol 14, Iss 2105, p

Modeling and Validation

2022 Volume 2105

Abstract: The spaceborne Global Navigation Satellite Systems Reflectometry (GNSS-R) offers versatile Earth surface observation. While the accuracy of the computed geometry, required for the implementation of the technique, degrades when Earth’s surface topography ... ...

Abstract	The spaceborne Global Navigation Satellite Systems Reflectometry (GNSS-R) offers versatile Earth surface observation. While the accuracy of the computed geometry, required for the implementation of the technique, degrades when Earth’s surface topography is complicated, previous studies ignored the effects of the local terrain surrounding the ideal specular point at a suppositional Earth reference surface. The surface slope and its aspect have been confirmed that it can lead to geolocation-related errors in the traditional radar altimetry, which will be even more intensified in tilt observations. In this study, the effect of large-scale slope on the spaceborne GNSS-R technique is investigated. We propose a new geometry computation strategy based on the property of ellipsoid to carry out forward and inverse calculations of path geometries. Moreover, it can be extended to calculate unusual reflected paths over versatile Earth’s topography by taking the surface slope and aspects into account. A simulation considering the slope effects demonstrates potential errors as large as meters to tens kilometers in geolocation and height estimations in the grazing observation condition over slopes. For validation, a single track over the Greenland surface received by the TechDemoSat 1 (TDS-1) satellite with a slope range from 0% to 1% was processed and analyzed. The results show that using the TanDEM-X 90 m Digital Elevation Model (DEM) as a reference, a slope of 0.6% at an elevation angle of 54 degrees can result in a geolocation inaccuracy of 10 km and a height error of 50 m. The proposed method in this study greatly reduces the standard deviation of geolocations of specular points from 4758 m to 367 m, and height retrievals from 28 m to 5.8 m. Applications associated with topography slopes, e.g., cryosphere could benefit from this method.
Keywords	GNSS-Reflectometry ; geometry computation ; topography slope ; specular point ; surface height estimation ; greenland ; Science ; Q
Subject code	550
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Millimeter to centimeter scale precision water-level monitoring using GNSS reflectometry: Application to the South-to-North Water Diversion Project, China

Wang, Xiaolei / He, Xiufeng / Xiao, Ruya / Song, Minfeng / Jia, Dongzheng

Remote sensing of environment. 2021 Nov., v. 265

2021

Abstract: Water-level monitoring is important for climate analysis, water resource planning, and monitoring of disasters, such as floods, droughts, and storm surges. The technology of global navigation satellite system-reflectometry (GNSS-R) has been demonstrated ... ...

Abstract	Water-level monitoring is important for climate analysis, water resource planning, and monitoring of disasters, such as floods, droughts, and storm surges. The technology of global navigation satellite system-reflectometry (GNSS-R) has been demonstrated previously and can be used to retrieve data on various water levels, such as sea, lake, river, and reservoir water levels. In this paper, we focus on the branch of GNSS-R that is based on the conventional geodetic receiver. In order to improve precision and promote the actual application, we present a multi-site multi-signal GNSS-R combination method. Furthermore, to address the phenomenon of “double peaks” in spectrograms of GPS L2P/L2W signal, we present a strategy to retrieve water levels from the L2P/L2W signal captured using Z-tracking method. Data of a GNSS network, which included a base station and three monitoring sites, established in a reservoir of the South-to-North Water Diversion Project were analyzed. The multi-site, multi-signal combination method was used to form a 6-h water level retrieval series and the retrievals showed a root mean square error (RMSE) of 6.0 mm. This is the first example of GNSS-R water-level retrieval achieving a millimeter to centimeter scale precision. The ability of the GNSS technology to simultaneously monitor water level and displacement based on the same GNSS network were also discussed and demonstrated. This study showed that GNSS-R could achieve high precision, high sampling, increased service, and lower cost, thereby representing a crucial progress in the practical application of the GNSS-R technology.
Keywords	climate ; environment ; lakes ; reflectometry ; rivers ; satellites ; storms ; China
Language	English
Dates of publication	2021-11
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	431483-9
ISSN	0034-4257
ISSN	0034-4257
DOI	10.1016/j.rse.2021.112645
Database	NAL-Catalogue (AGRICOLA)

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