scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenyi Xu ◽  
Tianda Chen ◽  
Yuwei Pei ◽  
Hao Guo ◽  
Zhuanyu Li ◽  
...  
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Shotgun Sequencing ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Cost Efficient ◽  
Taxonomic Assignments

Characterization of the bacterial composition and functional repertoires of microbiome samples is the most common application of metagenomics. Although deep whole-metagenome shotgun sequencing (WMS) provides high taxonomic resolution, it is generally cost-prohibitive for large longitudinal investigations. Until now, 16S rRNA gene amplicon sequencing (16S) has been the most widely used approach and usually cooperates with WMS to achieve cost-efficiency. However, the accuracy of 16S results and its consistency with WMS data have not been fully elaborated, especially by complicated microbiomes with defined compositional information. Here, we constructed two complex artificial microbiomes, which comprised more than 60 human gut bacterial species with even or varied abundance. Utilizing real fecal samples and mock communities, we provided solid evidence demonstrating that 16S results were of poor consistency with WMS data, and its accuracy was not satisfactory. In contrast, shallow whole-metagenome shotgun sequencing (shallow WMS, S-WMS) with a sequencing depth of 1 Gb provided outputs that highly resembled WMS data at both genus and species levels and presented much higher accuracy taxonomic assignments and functional predictions than 16S, thereby representing a better and cost-efficient alternative to 16S for large-scale microbiome studies.

Squalus clarkae sp. nov., a new dogfish shark from the Northwest Atlantic and Gulf of Mexico, with comments on the Squalus mitsukurii species complex

Zootaxa ◽  
2018 ◽  
Vol 4444 (2) ◽  
pp. 101 ◽  
Author(s):  
MARIAH O. PFLEGER ◽  
R. DEAN GRUBBS ◽  
CHARLES F. COTTON ◽  
TOBY S. DALY-ENGEL
Keyword(s):  
Gulf Of Mexico ◽  
Deep Water ◽  
Species Complex ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
Bootstrap Support ◽  
Interorbital Space ◽  
Low Genetic Diversity ◽  
Dogfish Shark ◽  
Reproductive Rates

Sharks of the genus Squalus have slow reproductive rates coupled with low genetic diversity, as is typical of deep-water sharks, making this group slow to rebound from depletion due to overfishing. The number of species within Squalus has been expanding recently due to increased attention on taxonomic revision, and a growing research focus on little-known deep-water sharks in general. Here we use genetics and morphology to describe a new species of dogfish shark, Squalus clarkae sp. nov. from the Gulf of Mexico (GoM) which replaces Squalus mitsukurii in this region, and place it in the context of congeners from the Atlantic and elsewhere. Previously, S. clarkae sp. nov. was considered a part of the Squalus mitsukurii species complex, a group of closely related but distinct species. We sequenced the mitochondrial cytochrome oxidase I and the NADH Dehydrogenase II gene of S. mitsukurii from the type location in Japan, S. clarkae sp. nov. from the GoM, as well as three closely related species (S. cubensis, S. blainville, and S. megalops) and S. cf. mitsukurii from Brazil. Squalus clarkae sp. nov. is genetically distinct from other species with significant statistical support (>98.6% bootstrap support/posterior probability), and 2.8% divergent from S. mitsukurii in the type location of Japan. Morphological estimates also revealed differences between S. clarkae sp. nov., S. mitsukurii, and other Atlantic Squalus species, with S. clarkae sp. nov. exhibiting a longer body, smaller interorbital space, shorter caudal fin, and a differently-proportioned first dorsal fin. In general, dogfish sharks in the Atlantic and GoM are characterized by similar but distinct morphology, significant genetic variation, and small species ranges. 

scholarly journals Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Brayon J. Fremin ◽  
Ami S. Bhatt
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Human Microbiome ◽  
Automated Analysis ◽  
Metagenomic Data ◽  
Coding Regions ◽  
Intergenic Regions ◽  
Computationally Intensive

Abstract Background Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations. Results We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. We validate the RNA expression of 177 of these candidate structures by analyzing small fragment RNA-seq data from four human fecal samples. Conclusions This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. Overall, our pipeline enables conservative predictions of thousands of novel candidate structured RNAs from human microbiomes.

scholarly journals Novel gut pathobionts confound results in a widely used mouse model of human inflammatory disease

2021 ◽  
Author(s):  
Samuel C. Forster ◽  
Simon Clare ◽  
Benjamin S. Beresford-Jones ◽  
Katherine Harcourt ◽  
George Notley ◽  
...  
Keyword(s):  
Mouse Model ◽  
Mouse Models ◽  
Large Scale ◽  
Bacterial Species ◽  
The Novel ◽  
Host Immune Responses ◽  
Causes Of Disease ◽  
Health And Disease ◽  
Inflammatory Bowel ◽  
Scale Experiment

The mammalian gut microbiota consists of hundreds of anaerobic bacterial species that shape intestinal homeostasis and influence host immune responses. Although the causal roles of specific human gut bacterial species in health and disease are emerging, the role of indigenous gut bacteria in driving immunophenotypic variability in mouse models of human disease remains poorly understood. We performed a large-scale experiment using 579 laboratory mice designed to identify and validate the causes of disease variability in the widely used dextran sulphate sodium (DSS) mouse model of inflammatory bowel disease. Using microbiome analysis, coupled with machine learning and targeted anaerobic culturing, we identified and isolated the novel gut pathobiont species Duncaniella muricolitica and Alistipes okayasuensis and fulfilled Koch’s postulates in mice to show that each pathobiont exerts dominant effects in the DSS model leading to variable treatment responses. We show these pathobiont species are common, but not ubiquitous, in mouse facilities around the world, raising experimental design opportunities for improved mouse models of human intestinal diseases.

Covalent Atomic Bridges Enable Unidirectional Enhancement of Electronic Transport in Aligned Carbon Nanotubes

2019 ◽  
Author(s):  
Mingguang Chen ◽  
Wangxiang Li ◽  
Anshuman Kumar ◽  
Guanghui Li ◽  
Mikhail Itkis ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Electrical Transport ◽  
Large Scale ◽  
The Novel ◽  
Electrical Measurements ◽  
Metal Atoms ◽  
Aligned Carbon Nanotubes ◽  
Transport Channels ◽  
Walled Carbon Nanotubes ◽  
Bulk Structures

<p>Interconnecting the surfaces of nanomaterials without compromising their outstanding mechanical, thermal, and electronic properties is critical in the design of advanced bulk structures that still preserve the novel properties of their nanoscale constituents. As such, bridging the p-conjugated carbon surfaces of single-walled carbon nanotubes (SWNTs) has special implications in next-generation electronics. This study presents a rational path towards improvement of the electrical transport in aligned semiconducting SWNT films by deposition of metal atoms. The formation of conducting Cr-mediated pathways between the parallel SWNTs increases the transverse (intertube) conductance, while having negligible effect on the parallel (intratube) transport. In contrast, doping with Li has a predominant effect on the intratube electrical transport of aligned SWNT films. Large-scale first-principles calculations of electrical transport on aligned SWNTs show good agreement with the experimental electrical measurements and provide insight into the changes that different metal atoms exert on the density of states near the Fermi level of the SWNTs and the formation of transport channels. </p>

scholarly journals IoT Traffic: Modeling and Measurement Experiments

IoT ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 140-162
Author(s):  
Hung Nguyen-An ◽  
Thomas Silverston ◽  
Taku Yamazaki ◽  
Takumi Miyoshi
Keyword(s):  
Smart Home ◽  
Large Scale ◽  
Traffic Modeling ◽  
The Novel ◽  
Network Behavior ◽  
Performance Accuracy ◽  
Traffic Generator ◽  
Multiple Devices ◽  
Iot Devices ◽  
The Internet Of Things

We now use the Internet of things (IoT) in our everyday lives. The novel IoT devices collect cyber–physical data and provide information on the environment. Hence, IoT traffic will count for a major part of Internet traffic; however, its impact on the network is still widely unknown. IoT devices are prone to cyberattacks because of constrained resources or misconfigurations. It is essential to characterize IoT traffic and identify each device to monitor the IoT network and discriminate among legitimate and anomalous IoT traffic. In this study, we deployed a smart-home testbed comprising several IoT devices to study IoT traffic. We performed extensive measurement experiments using a novel IoT traffic generator tool called IoTTGen. This tool can generate traffic from multiple devices, emulating large-scale scenarios with different devices under different network conditions. We analyzed the IoT traffic properties by computing the entropy value of traffic parameters and visually observing the traffic on behavior shape graphs. We propose a new method for identifying traffic entropy-based devices, computing the entropy values of traffic features. The method relies on machine learning to classify the traffic. The proposed method succeeded in identifying devices with a performance accuracy up to 94% and is robust with unpredictable network behavior with traffic anomalies spreading in the network.

scholarly journals Multi-Objective Optimization of Integrated Civilian-Military Scheduling of Medical Supplies for Epidemic Prevention and Control

Healthcare ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 126
Author(s):  
Hai-Feng Ling ◽  
Zheng-Lian Su ◽  
Xun-Lin Jiang ◽  
Yu-Jun Zheng
Keyword(s):  
Prevention And Control ◽  
Large Scale ◽  
Medical Services ◽  
The Novel ◽  
Multi Objective ◽  
Medical Supplies ◽  
Problem Instances ◽  
Novel Coronavirus ◽  
And Control ◽  
Minimum Ratio

In a large-scale epidemic, such as the novel coronavirus pneumonia (COVID-19), there is huge demand for a variety of medical supplies, such as medical masks, ventilators, and sickbeds. Resources from civilian medical services are often not sufficient for fully satisfying all of these demands. Resources from military medical services, which are normally reserved for military use, can be an effective supplement to these demands. In this paper, we formulate a problem of integrated civilian-military scheduling of medical supplies for epidemic prevention and control, the aim of which is to simultaneously maximize the overall satisfaction rate of the medical supplies and minimize the total scheduling cost, while keeping a minimum ratio of medical supplies reservation for military use. We propose a multi-objective water wave optimization (WWO) algorithm in order to efficiently solve this problem. Computational results on a set of problem instances constructed based on real COVID-19 data demonstrate the effectiveness of the proposed method.

scholarly journals Re-Evaluation of the Podosphaera tridactyla Species Complex in Australia

2021 ◽  
Vol 7 (3) ◽  
pp. 171
Author(s):  
Reannon L. Smith ◽  
Tom W. May ◽  
Jatinder Kaur ◽  
Tim I. Sawbridge ◽  
Ross C. Mann ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Species Complex ◽  
Taxonomic Revision ◽  
Stone Fruit ◽  
Prunus Species ◽  
Wide Range ◽  
Unidentified Species ◽  
The Rose ◽  
Generation Sequencing

The Podosphaera tridactyla species complex is highly variable morphologically and causes powdery mildew on a wide range of Prunus species, including stone fruit. A taxonomic revision of the Po. tridactyla species complex in 2020 identified 12 species, seven of which were newly characterised. In order to clarify which species of this complex are present in Australia, next generation sequencing was used to isolate the fungal ITS+28S and host matK chloroplast gene regions from 56 powdery mildew specimens of stone fruit and ornamental Prunus species accessioned as Po. tridactyla or Oidium sp. in Australian reference collections. The specimens were collected in Australia, Switzerland, Italy and Korea and were collected from 1953 to 2018. Host species were confirmed using matK phylogenetic analysis, which identified that four had been misidentified as Prunus but were actually Malusprunifolia. Podosphaera species were identified using ITS+28S phylogenetic analysis, recognising three Podosphaera species on stone fruit and related ornamental Prunus hosts in Australia. These were Po.pannosa, the rose powdery mildew, and two species in the Po. tridactyla species complex: Po. ampla, which was the predominant species, and a previously unidentified species from peach, which we describe here as Po. cunningtonii.

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