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Perspective: The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights
- Elizabeth A. Grice
Genome Res. October 2015 25: 1514-1520; doi:10.1101/gr.191320.115
..., while phages that enter lysogeny may participate in horizontal gene transfer events that confer pathogenicity, virulence, and antibiotic resistance to their hosts. Due largely to technical limitations associated with low bioburden on the skin, the viruses that inhabit the skin and interact...
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ARTICLE: The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation
- Nicholas R. Thomson,
- Corin Yeats,
- Kenneth Bell,
- Matthew T.G. Holden,
- Stephen D. Bentley,
- Morag Livingstone,
- Ana M. Cerdeño-Tárraga,
- Barbara Harris,
- Jon Doggett,
- Doug Ormond,
- Karen Mungall,
- Kay Clarke,
- Theresa Feltwell,
- Zahra Hance,
- Mandy Sanders,
- Michael A. Quail,
- Claire Price,
- Bart G. Barrell,
- Julian Parkhill,
- and David Longbottom
Genome Res. May 2005 15: 629-640; Published in Advance April 18, 2005, doi:10.1101/gr.3684805
...pathway, appearing as secretory vacuoles to the host cell ( Hackstadt et al. 1997 ). RBs transform back into EBs 2–3 d after infection (depending on species) and are then released by lysis or exocytosis to complete the infectious process. EBs can be spread by aerosols, through ingestion, and by direct...
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LETTER: EST Mining and Functional Expression Assays Identify Extracellular Effector Proteins From the Plant Pathogen Phytophthora
- Trudy A. Torto,
- Shuang Li,
- Allison Styer,
- Edgar Huitema,
- Antonino Testa,
- Neil A.R. Gow,
- Pieter van West,
- and Sophien Kamoun
Genome Res. July 2003 13: 1675-1685; doi:10.1101/gr.910003
...could be secreted and thus delivered to plant cells during infection. Analyses of the response induced by the crn cDNAs in various plants suggest that they are general elicitors that trigger necrotic responses nonspecifically in both resistant Nicotiana species and the susceptible host plant tomato...
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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
...protein to which no host antibodies have been produced, contributing to cyclical parasitaemia. Parasites taken up by the tsetse during blood meals differentiate in the fly midgut to the procyclic form (PF), which replaces all VSGs with procyclin surface proteins (Roditi and Liniger 2002).The T. brucei...
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Letter: Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
- Thomas J. Sharpton,
- Jason E. Stajich,
- Steven D. Rounsley,
- Malcolm J. Gardner,
- Jennifer R. Wortman,
- Vinita S. Jordar,
- Rama Maiti,
- Chinnappa D. Kodira,
- Daniel E. Neafsey,
- Qiandong Zeng,
- Chiung-Yu Hung,
- Cody McMahan,
- Anna Muszewska,
- Marcin Grynberg,
- M. Alejandra Mandel,
- Ellen M. Kellner,
- Bridget M. Barker,
- John N. Galgiani,
- Marc J. Orbach,
- Theo N. Kirkland,
- Garry T. Cole,
- Matthew R. Henn,
- Bruce W. Birren,
- and John W. Taylor
Genome Res. October 2009 19: 1722-1731; Published in Advance August 28, 2009, doi:10.1101/gr.087551.108
...are not typical soil fungi in that they maintain a close association with keratin-rich animals both during infection of a living host and after the host has died by growing through the carcass as mycelium. Additional evidence about lifecycle may be found in the deficit of dehydrogenases and HET proteins...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...for herbivores. The plants consumed by herbivores comprise complex polysaccharides that cannot be digested by mammalian enzymes. However, microorganisms in the herbivore gut can ferment these compounds to produce metabolites that are used easily by their host. The importance of microorganisms for plant...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...with the strongest association with human quasi-prime-containing genes, have not been observed in other species (Burns 2004). Similarly, a strong association of scoliosis, a bipedal-specific disorder (de Reuver et al. 2021), and of hepatitis/hepatitis B, viral disease derived from a humanoid host pathogen (Devaux et...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...in bacteria reads (Fig. 3C,D; Supplemental Figs. S10, S12). This pattern could be used to distinguish the host and bacterial reads, and help to remove DNA contamination from bacterial DNA, or vice versa.Hammerhead can de novo identify all potential methylation sites with one command, from FASTQ/FASTA input...
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Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
...variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African...
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Research: The altered landscape of the human skin microbiome in patients with primary immunodeficiencies
- Julia Oh,
- Alexandra F. Freeman,
- NISC Comparative Sequencing Program,
- Morgan Park,
- Robert Sokolic,
- Fabio Candotti,
- Steven M. Holland,
- Julia A. Segre,
- and Heidi H. Kong
Genome Res. December 2013 23: 2103-2114; Published in Advance October 29, 2013, doi:10.1101/gr.159467.113
...immunodeficiency (PID) patients suffer recurrent microbial infections, providing a unique opportunity to address this issue. To investigate the potential influence of host immunity on the skin microbiome, we examined skin microbiomes in patients with rare monogenic PIDs: hyper-IgE (STAT3-deficient), Wiskott...

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