Tourlousse, Dieter M. Narita, Koji Miura, Takamasa Sakamoto, Mitsuo Ohashi, Akiko Shiina, Keita Matsuda, Masami Miura, Daisuke Shimamura, Mamiko Ohyama, Yoshifumi
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Published in
Microbiome
BackgroundValidation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of hu...
Ceja-Navarro, Javier A. Wang, Yuan Ning, Daliang Arellano, Abelardo Ramanculova, Leila Yuan, Mengting Maggie Byer, Alyssa Craven, Kelly D. Saha, Malay C. Brodie, Eoin L.
...
Published in
Microbiome
BackgroundDespite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the ...
Borchmann, Sven
Published in
Microbiome
BackgroundHost tissue infections by bacteria and viruses can cause cancer. Known viral carcinogenic mechanisms are disruption of the host genome via genomic integration and expression of oncogenic viral proteins. An important bacterial carcinogenic mechanism is chronic inflammation. Massively parallel sequencing now routinely generates datasets lar...
Barretto, Sharon Ann Lasserre, Frederic Huillet, Marine Régnier, Marion Polizzi, Arnaud Lippi, Yannick Fougerat, Anne Person, Elodie Bruel, Sandrine Bétoulières, Colette
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Published in
Microbiome
BackgroundThe gut microbiota–intestine–liver relationship is emerging as an important factor in multiple hepatic pathologies, but the hepatic sensors and effectors of microbial signals are not well defined.ResultsBy comparing publicly available liver transcriptomics data from conventional vs. germ-free mice, we identified pregnane X receptor (PXR, ...
Mu, Andre McDonald, Daniel Jarmusch, Alan K. Martino, Cameron Brennan, Caitriona Bryant, Mackenzie Humphrey, Gregory C. Toronczak, Julia Schwartz, Tara Nguyen, Dominic
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Published in
Microbiome
BackgroundInfectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood.Result...
Zuo, Tao Liu, Qin Zhang, Fen Yeoh, Yun Kit Wan, Yating Zhan, Hui Lui, Grace C. Y. Chen, Zigui Li, Amy Y. L. Cheung, Chun Pan
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Published in
Microbiome
BackgroundCoronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively kno...
Williamson, Kayla M. Wagner, Brandie D. Robertson, Charles E. Stevens, Mark J. Sontag, Marci K. Mourani, Peter M. Harris, J. Kirk
Published in
Microbiome
BackgroundThe objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing. Two PCR protocols (standard and modified) were examined in airway samples where we observed a large range in bacterial load (3.1–...
Restrepo, Leda Domínguez-Borbor, Cristóbal Bajaña, Leandro Betancourt, Irma Rodríguez, Jenny Bayot, Bonny Reyes, Alejandro
Published in
Microbiome
BackgroundAcute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to develop alternatives to prophylactic antibiotics use, such as the application of probiotics. To assess the potential to use pro...
Guerin, Emma Shkoporov, Andrey N. Stockdale, Stephen R. Comas, Joan Colom Khokhlova, Ekaterina V. Clooney, Adam G. Daly, Karen M. Draper, Lorraine A. Stephens, Niamh Scholz, Dimitri
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Published in
Microbiome
BackgroundThe gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual’s core virome. Based on met...
Cambon-Bonavita, Marie-Anne Aubé, Johanne Cueff-Gauchard, Valérie Reveillaud, Julie
Published in
Microbiome
BackgroundFree-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria prese...
