Journal of Microbiology

Journal Articles

Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids: Dongjin Choi , Yoonsoo Hahn; J. Microbiol. 2023;61(10):917-927. Published online October 16, 2023; DOI: https://doi.org/10.1007/s12275-023-00083-z

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Potyvirids, members of the family Potyviridae, produce the P3N-PIPO protein, which is crucial for the cell-to-cell transport of viral genomic RNAs. The production of P3N-PIPO requires an adenine (A) insertion caused by RNA polymerase slippage at a conserved GAA AAA A ( GA6) sequence preceding the PIPO open reading frame. Presently, the slippage rate of RNA polymerase has been estimated in only a few potyvirids, ranging from 0.8 to 2.1%. In this study, we analyzed publicly available plant RNA-seq data and identified 19 genome contigs from 13 distinct potyvirids. We further investigated the RNA polymerase slippage rates at the GA6 motif. Our analysis revealed that the frequency of the A insertion variant ranges from 0.53 to 4.07% in 11 potyviruses (genus Potyvirus). For the two macluraviruses (genus Macluravirus), the frequency of the A insertion variant was found to be 0.72% and 10.96% respectively. Notably, the estimated RNA polymerase slippage rates for 12 out of the 13 investigated potyvirids were reported for the first time in this study. Our findings underscore the value of plant RNA-seq data for quantitative analysis of potyvirid genome variants, specifically at the GA6 slippage site, and contribute to a more comprehensive understanding of the RNA polymerase slippage phenomenon in potyvirids.

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Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data
Dongjin Choi, Hyerin Park, Seungwoo Baek, Myeung Seok Choi, Sylvain Legay, Gea Guerriero, Jean-François Hausman, Yoonsoo Hahn
Acta Virologica.2025;[Epub] CrossRef
Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins
Veronika Hýsková, Kateřina Bělonožníková, Josef Chmelík, Hana Hoffmeisterová, Noemi Čeřovská, Tomáš Moravec, Helena Ryšlavá
Plants.2024; 13(9): 1236. CrossRef
Reconceptualizing transcriptional slippage in plant RNA viruses
Adrian A. Valli, María Luisa Domingo-Calap, Alfonso González de Prádena, Juan Antonio García, Hongguang Cui, Cécile Desbiez, Juan José López-Moya, Shou-Wei Ding, Andrew Firth
mBio.2024;[Epub] CrossRef

Comparative genomics analysis of Pediococcus acidilactici species: Zhenzhen Li , Qi Song , Mingming Wang , Junli Ren , Songling Liu , Shancen Zhao; J. Microbiol. 2021;59(6):573-583. Published online May 15, 2021; DOI: https://doi.org/10.1007/s12275-021-0618-6

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Abstract

Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.

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Pediococcus acidilactici Y01 reduces HFD-induced obesity via altering gut microbiota and metabolomic profiles and modulating adipose tissue macrophage M1/M2 polarization
Yujing Wang, Yu Xue, Huan Xu, Qian Zhu, Kaili Qin, Zhonglei He, Aixiang Huang, Min Mu, Xinrong Tao
Food & Function.2025;[Epub] CrossRef
Draft genome sequence of Pediococcus acidilactici 3G3 isolated from Philippine fermented pork
Zachary B. Lara, Mia Beatriz C. Amoranto, Francisco B. Elegado, Leslie Michelle M. Dalmacio, Marilen Parungao Balolong, Catherine Putonti
Microbiology Resource Announcements.2024;[Epub] CrossRef
The Potential of Pediococcus acidilactici Cell-Free Supernatant as a Preservative in Food Packaging Materials
Katherine Kho, Adinda Darwanti Kadar, Mario Donald Bani, Ihsan Tria Pramanda, Leon Martin, Matthew Chrisdianto, Ferren Pratama, Putu Virgina Partha Devanthi
Foods.2024; 13(5): 644. CrossRef
The complete genome sequences of the two novel probiotics were isolated from the human gut microbiota: Pediococcus acidilactici WNYM01 and Pediococcus acidilactici WNYM02, vitamin B9, and B2-producers
Wagiha S. Elkalla, Yasser M. Ragab, Mohamed A. Ramadan, Nahla M. Mansour
Egyptian Pharmaceutical Journal.2024; 23(4): 702. CrossRef
Effects of Pediococcus acidilactici and Rhizopus Oryzae on protein degradation and flavor formation in fermented mutton sausages
Zihan Li, Wei Su, Yingchun Mu, Qi Qi, Li Jiang
LWT.2024; 213: 117075. CrossRef
Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs
Shaoqi Tian, Yinhong Jiang, Qiannan Han, Chuang Meng, Feng Ji, Bin Zhou, Manhong Ye
Probiotics and Antimicrobial Proteins.2024;[Epub] CrossRef
Effect of ginsenoside fermented by Pediococcus acidilactici XM-06 on preventing diarrhea in mice via regulating intestinal barrier function and gut microbiota
Wen-Man Xu, Qi Liu, Si-Yao Fan, Zi-Xin Wang, Shi-Rui Lu, Jie Liu, Hong-Jie Piao, Wenxiu Ji, Wei-Wei Dong
Journal of Functional Foods.2024; 123: 106594. CrossRef
Population and functional genomics of lactic acid bacteria, an important group of food microorganism: Current knowledge, challenges, and perspectives
Weicheng Li, Qiong Wu, Lai‐yu Kwok, Heping Zhang, Renyou Gan, Zhihong Sun
Food Frontiers.2024; 5(1): 3. CrossRef
CRISPR-Cas systems of lactic acid bacteria and applications in food science
Yanhua Cui, Xiaojun Qu
Biotechnology Advances.2024; 71: 108323. CrossRef
Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics
Ismail Gumustop, Fatih Ortakci
Frontiers in Microbiology.2023;[Epub] CrossRef
Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods
Ruhong Wang, Junrui Wu, Nan Jiang, Hao Lin, Feiyu An, Chen Wu, Xiqing Yue, Haisu Shi, Rina Wu
Critical Reviews in Food Science and Nutrition.2023; 63(5): 569. CrossRef
Changes in Lacto-Fermented Agaricus bisporus (White and Brown Varieties) Mushroom Characteristics, including Biogenic Amine and Volatile Compound Formation
Elena Bartkiene, Paulina Zarovaite, Vytaute Starkute, Ernestas Mockus, Egle Zokaityte, Gintare Zokaityte, João Miguel Rocha, Romas Ruibys, Dovile Klupsaite
Foods.2023; 12(13): 2441. CrossRef
Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6, Two Bacteriocinogenic Isolated Strains from Andalusian Spontaneous Fermented Sausages
José García-López, Claudia Teso-Pérez, Antonio Martín-Platero, Juan Peralta-Sánchez, Juristo Fonollá-Joya, Manuel Martínez-Bueno, Alberto Baños
Foods.2023; 12(13): 2445. CrossRef
Exploring the impact of initial moisture content on microbial community and flavor generation in Xiaoqu baijiu fermentation
Huan Wang, Chunhong Sun, Shengzhi Yang, Yulei Ruan, Linjie Lyu, Xuewu Guo, Xiaole Wu, Yefu Chen
Food Chemistry: X.2023; 20: 100981. CrossRef
Screening and Constructing a Library of Promoter-5′-UTR Complexes with Gradient Strength in Pediococcus acidilactici
Yize Jia, Chao Huang, Yin Mao, Shenghu Zhou, Yu Deng
ACS Synthetic Biology.2023; 12(6): 1794. CrossRef
Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods
Basista Rabina Sharma, Prakash M. Halami, Jyoti Prakash Tamang
Food Science and Biotechnology.2022; 31(1): 1. CrossRef
Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections
Hassan M. Al-Emran, Jannatul Ferdouse Moon, Md. Liton Miah, Nigar Sultana Meghla, Rine Christopher Reuben, Mohammad Jashim Uddin, Habiba Ibnat, Shovon Lal Sarkar, Pravas Chandra Roy, M. Shaminur Rahman, A. S. M. Rubayet Ul Alam, Ovinu Kibria Islam, Iqbal
Scientific Reports.2022;[Epub] CrossRef
Production of Antibacterial Agents and Genomic Characteristics of Probiotics Strains for the Foodborne Pathogen Control
Su Jin Kim, Jin Song Shin, Han Sol Park, Ji Seop Song, Ki Won Lee, Woo-Suk Bang, Tae Jin Cho
Current Topic in Lactic Acid Bacteria and Probiotics.2022; 8(1): 1. CrossRef

The effects of cigarettes and alcohol on intestinal microbiota in healthy men: Renbin Lin , Yawen Zhang , Luyi Chen , Yadong Qi , Jiamin He , Mengjia Hu , Ying Zhang , Lina Fan , Tao Yang , Lan Wang , Misi Si , Shujie Chen; J. Microbiol. 2020;58(11):926-937. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0006-7

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Abstract

Human intestinal microbiota is affected by the exogenous microenvironment. This study aimed to determine the effects of cigarettes and alcohol on the gut microbiota of healthy men. In total, 116 healthy male subjects were enrolled and divided into four groups: non-smoking and non-drinking (Group A), smoking only (Group B), drinking only (Group C), and smoking and drinking combined (Group D). Fecal samples were collected and sequenced using 16S rRNA to analyze the microbial composition. Short-chain fatty acid (SCFAs) levels in feces were determined by gas chromatography. We found that cigarette and alcohol consumptions can alter overall composition of gut microbiota in healthy men. The relative abundances of phylum Bacteroidetes and Firmicutes and more than 40 genera were changed with cigarette and alcohol consumptions. SCFAs decreased with smoking and alcohol consumption. Multivariate analysis indicated that when compared with group A, group B/C/D had higher Bacteroides, and lower Phascolarctobacterium, Ruminococcaceae_ UCG-002, Ruminococcaceae_UCG-003, and Ruminiclostridium_ 9 regardless of BMI and age. Additionally, the abundance of Bacteroides was positively correlated with the smoking pack-year (r = 0.207, p < 0.05), the abundance of predicted pathway of bacterial toxins (r = 0.3672, p < 0.001) and the level of carcinoembryonic antigen in host (r = 0.318, p < 0.01). Group D shared similar microbial construction with group B, but exerted differences far from group C with lower abundance of Haemophilus. These results demonstrated that cigarette and alcohol consumption separately affected the intestinal microbiota and function in healthy men; furthermore, the co-occurrence of cigarette and alcohol didn’t exacerbate the dysbiosis and cigarette played the predominated role on the alteration.

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International Journal of Molecular Sciences.2022; 24(1): 252. CrossRef
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Research Support, Non-U.S. Gov'ts

Microbial Community on Healthy and Diseased Leaves of an Invasive Plant Eupatorium adenophorum in Southwest China: Zhen-Xin Zhou , Huan Jiang , Chen Yang , Ming-Zhi Yang , Han-Bo Zhang; J. Microbiol. 2010;48(2):139-145. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-9185-y

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Abstract: Invasive plants have caused great economic losses and environmental problems worldwide. Eupatorium adenophorum is one of the most invasive weeds in China. To better understand its invasive mechanisms, in the present paper, the microbial communities of healthy and diseased leaves of E. adenophorum were obtained using both culture-independent and -dependent methods and their diversities were compared. The bacteria obtained from culture-independent method belong to Proteobacteria (95.8%), Actinobacteria (2.1%), and Firmicutes (2.1%) and fungi belong to Ascomycota (65.2%) and Basidiomycota (34.8%). Very few overlapped microbial species were found by culture-dependent and -independent methods. Healthy leaves display higher bacterial diversity than diseased leaves. Phylogenetic structures are very different between healthy and diseased phyllosphere microbial communities. Bacteria close to Acinetobacter and Pseudomonas were dominant on healthy leaves, whereas those close to Shigella were dominant on diseased leaves. 52.9% of fungal clones from healthy leaves were Ustilaginomycetes, close to Rhodotorula phylloplana and uncultured basidomycete; by contrast, 60% of clones from diseased leaves were Lecanoromycetes, close to Umbilicaria muehlenbergii. No bacteria but four fungal strains phylogenetically close to Myrothecium sp. and Alternaria alternate were pathogenic to seedlings and detached leaves of the invasive plant. Therefore, this plant may be resistant to pathogens from bacteria but not fungi in its introduced range.

Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People: Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(5):491-501. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0199-7

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Abstract

The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

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Matthew E. Rhodes, Allyson D. Pace, Menny M. Benjamin, Heather Ghent, Katherine S. Dawson
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A. Krawczyk, T. Gosiewski, B. Zapała, K. Kowalska-Duplaga, D. Salamon
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Rokhsareh Mohammadzadeh, Alexander Mahnert, Stefanie Duller, Christine Moissl-Eichinger
Current Opinion in Microbiology.2022; 67: 102146. CrossRef
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Hosseinali Abdi, Dor Mohammad Kordi-Tamandani, Milad Lagzian, Alireza Bakhshipour
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The host-associated archaeome
Guillaume Borrel, Jean-François Brugère, Simonetta Gribaldo, Ruth A. Schmitz, Christine Moissl-Eichinger
Nature Reviews Microbiology.2020; 18(11): 622. CrossRef
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mSystems.2020;[Epub] CrossRef
The gut mycobiota of rural and urban individuals is shaped by geography
Mubanga Hellen Kabwe, Surendra Vikram, Khodani Mulaudzi, Janet K. Jansson, Thulani P. Makhalanyane
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Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research
Katarzyna B. Hooks, Maureen A. O'Malley
Journal of Eukaryotic Microbiology.2020; 67(2): 279. CrossRef
The human gut archaeome: identification of diverse haloarchaea in Korean subjects
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Microbiome.2020;[Epub] CrossRef
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Pei Pei Chong, Voon Kin Chin, Chung Yeng Looi, Won Fen Wong, Priya Madhavan, Voon Chen Yong
Frontiers in Microbiology.2019;[Epub] CrossRef
Archaea Are Interactive Components of Complex Microbiomes
Christine Moissl-Eichinger, Manuela Pausan, Julian Taffner, Gabriele Berg, Corinna Bang, Ruth A. Schmitz
Trends in Microbiology.2018; 26(1): 70. CrossRef
Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients
Ibrahim Hamad, Rita Abou Abdallah, Isabelle Ravaux, Saadia Mokhtari, Hervé Tissot-Dupont, Caroline Michelle, Andreas Stein, Jean-Christophe Lagier, Didier Raoult, Fadi Bittar, Brenda A. Wilson
PLOS ONE.2018; 13(1): e0191913. CrossRef
Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies
Isabelle Laforest-Lapointe, Marie-Claire Arrieta
mSystems.2018;[Epub] CrossRef
Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut
Saber Khelaifia, Aurelia Caputo, Claudia Andrieu, Frederique Cadoret, Nicholas Armstrong, Caroline Michelle, Jean-Christophe Lagier, Felix Djossou, Pierre-Edouard Fournier, Didier Raoult
Extremophiles.2018; 22(3): 485. CrossRef
Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638
Antonia Denis, Mario Martínez-Núñez, Silvia Tenorio-Salgado, Ernesto Perez-Rueda
Life.2018; 8(4): 40. CrossRef
Fungi in the healthy human gastrointestinal tract
Heather E. Hallen-Adams, Mallory J. Suhr
Virulence.2017; 8(3): 352. CrossRef
Archaea: Essential inhabitants of the human digestive microbiota
Vanessa Demonfort Nkamga, Bernard Henrissat, Michel Drancourt
Human Microbiome Journal.2017; 3: 1. CrossRef
First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
Kaisa Koskinen, Manuela R. Pausan, Alexandra K. Perras, Michael Beck, Corinna Bang, Maximilian Mora, Anke Schilhabel, Ruth Schmitz, Christine Moissl-Eichinger, Christa M. Schleper, Janet K. Jansson
mBio.2017;[Epub] CrossRef
Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
Kasie Raymann, Andrew H. Moeller, Andrew L. Goodman, Howard Ochman, Susannah Green Tringe
mSphere.2017;[Epub] CrossRef
Forgotten fungi—the gut mycobiome in human health and disease
Chloe E. Huseyin, Paul W. O’Toole, Paul D. Cotter, Pauline D. Scanlan
FEMS Microbiology Reviews.2017; 41(4): 479. CrossRef
Human age and skin physiology shape diversity and abundance of Archaea on skin
Christine Moissl-Eichinger, Alexander J. Probst, Giovanni Birarda, Anna Auerbach, Kaisa Koskinen, Peter Wolf, Hoi-Ying N. Holman
Scientific Reports.2017;[Epub] CrossRef
Mucosal Interactions between Genetics, Diet, and Microbiome in Inflammatory Bowel Disease
Abigail Basson, Ashley Trotter, Alex Rodriguez-Palacios, Fabio Cominelli
Frontiers in Immunology.2016;[Epub] CrossRef
Microbiotes et métagénomique
Jean Weissenbach, Abdelghani Sghir
médecine/sciences.2016; 32(11): 937. CrossRef
Bioinformatics-based study on prokaryotic, archaeal and eukaryotic nucleic acid-binding proteins for identification of low-complexity and intrinsically disordered regions
Birendra Singh Yadav, Swati Singh, Prashant Kumar, Devika Mathur, Raj Kumar Meena, Rishij Kumar Agrawal, Ashutosh Mani
Frontiers in Life Science.2016; 9(1): 2. CrossRef
Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods
I. Hamad, D. Raoult, F. Bittar
Parasite Immunology.2016; 38(1): 12. CrossRef
Accounting for reciprocal host–microbiome interactions in experimental science
Thaddeus S. Stappenbeck, Herbert W. Virgin
Nature.2016; 534(7606): 191. CrossRef
Current and Past Strategies for Bacterial Culture in Clinical Microbiology
Jean-Christophe Lagier, Sophie Edouard, Isabelle Pagnier, Oleg Mediannikov, Michel Drancourt, Didier Raoult
Clinical Microbiology Reviews.2015; 28(1): 208. CrossRef
Digestive tract mycobiota: A source of infection
N. Gouba, M. Drancourt
Médecine et Maladies Infectieuses.2015; 45(1-2): 9. CrossRef
Archaea associated with human surfaces: not to be underestimated
Corinna Bang, Ruth A. Schmitz, Franz Narberhaus
FEMS Microbiology Reviews.2015; 39(5): 631. CrossRef
Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water
Asja Korajkic, Laura Wegener Parfrey, Brian R. McMinn, Yoshiki Vazquez Baeza, Will VanTeuren, Rob Knight, Orin C. Shanks
Water Research.2015; 69: 30. CrossRef
Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans
Timothy Heisel, Heather Podgorski, Christopher M. Staley, Dan Knights, Michael J. Sadowsky, Cheryl A. Gale, Megan D. Lenardon
PLOS ONE.2015; 10(2): e0116705. CrossRef
Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions
Prem Prashant Chaudhary, Nadia Gaci, Guillaume Borrel, Paul W. O’Toole, Jean-François Brugère
Applied Microbiology and Biotechnology.2015; 99(14): 5801. CrossRef
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Nina Gouba, Didier Raoult, Michel Drancourt, Kirsten Nielsen
PLoS ONE.2014; 9(9): e106994. CrossRef
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Rosine E. Tiodjio, Akihiro Sakatoku, Akihiro Nakamura, Daisuke Tanaka, Wilson Y. Fantong, Kamtchueng B. Tchakam, Gregory Tanyileke, Takeshi Ohba, Victor J. Hell, Minoru Kusakabe, Shogo Nakamura, Akira Ueda
Scientific Reports.2014;[Epub] CrossRef
Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey
Ibrahim Hamad, Mamadou B. Keita, Martine Peeters, Eric Delaporte, Didier Raoult, Fadi Bittar
Scientific Reports.2014;[Epub] CrossRef
The microbial eukaryoteBlastocystisis a prevalent and diverse member of the healthy human gut microbiota
Pauline D. Scanlan, Christen R. Stensvold, Mirjana Rajilić-Stojanović, Hans G.H.J. Heilig, Willem M. De Vos, Paul W. O'Toole, Paul D. Cotter
FEMS Microbiology Ecology.2014; 90(1): 326. CrossRef
The first 1000 cultured species of the human gastrointestinal microbiota
Mirjana Rajilić-Stojanović, Willem M. de Vos
FEMS Microbiology Reviews.2014; 38(5): 996. CrossRef
Methanogens, Methane and Gastrointestinal Motility
Konstantinos Triantafyllou, Christopher Chang, Mark Pimentel
Journal of Neurogastroenterology and Motility.2014; 20(1): 31. CrossRef
Archaea and the human gut: New beginning of an old story
Nadia Gaci, Guillaume Borrel, William Tottey, Paul William O’Toole, Jean-François Brugère
World Journal of Gastroenterology.2014; 20(43): 16062. CrossRef
Age, Dietary Fiber, Breath Methane, and Fecal Short Chain Fatty Acids Are Interrelated in Archaea-Positive Humans1–3
Judlyn Fernandes, Angela Wang, Wen Su, Sari Rahat Rozenbloom, Amel Taibi, Elena M. Comelli, Thomas M.S. Wolever
The Journal of Nutrition.2013; 143(8): 1269. CrossRef
Gastrointestinal Colonization of Fungi
Andrew Y. Koh
Current Fungal Infection Reports.2013; 7(2): 144. CrossRef
Plant and Fungal Diversity in Gut Microbiota as Revealed by Molecular and Culture Investigations
Nina Gouba, Didier Raoult, Michel Drancourt, Yolanda Sanz
PLoS ONE.2013; 8(3): e59474. CrossRef
Gut and Root Microbiota Commonalities
Shamayim T. Ramírez-Puebla, Luis E. Servín-Garcidueñas, Berenice Jiménez-Marín, Luis M. Bolaños, Mónica Rosenblueth, Julio Martínez, Marco Antonio Rogel, Ernesto Ormeño-Orrillo, Esperanza Martínez-Romero
Applied and Environmental Microbiology.2013; 79(1): 2. CrossRef
Bacterial diversity of cheonggukjang, a traditional Korean fermented food, analyzed by barcoded pyrosequencing
Young-Do Nam, Sung-Hun Yi, Seong-Il Lim
Food Control.2012; 28(1): 135. CrossRef
The domain Archaea in human mucosal surfaces
F. Matarazzo, A.C. Ribeiro, M. Faveri, C. Taddei, M.B. Martinez, M.P.A. Mayer
Clinical Microbiology and Infection.2012; 18(9): 834. CrossRef
Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts
James Angus Chandler, Jonathan A. Eisen, Artyom Kopp
Applied and Environmental Microbiology.2012; 78(20): 7327. CrossRef
Hydrogenotrophic microbiota distinguish native Africans from African and European Americans
Gerardo M. Nava, Franck Carbonero, Junhai Ou, Ann C. Benefiel, Stephen J. O'Keefe, H. Rex Gaskins
Environmental Microbiology Reports.2012; 4(3): 307. CrossRef
Molecular Detection of Eukaryotes in a Single Human Stool Sample from Senegal
Ibrahim Hamad, Cheikh Sokhna, Didier Raoult, Fadi Bittar, Jonathan H. Badger
PLoS ONE.2012; 7(7): e40888. CrossRef
Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of bacterial community structure in the food, intestines, and feces of earthworms
Sung Wook Hong, Ju Sam Lee, Kun Sub Chung
The Journal of Microbiology.2011; 49(4): 544. CrossRef
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Páraic Ó Cuív, Daniel Aguirre de Cárcer, Michelle Jones, Eline S. Klaassens, Daniel L. Worthley, Vicki L. J. Whitehall, Seungha Kang, Christopher S. McSweeney, Barbara A. Leggett, Mark Morrison
Microbial Ecology.2011; 61(2): 353. CrossRef
Microbial community and metabolomic comparison of irritable bowel syndrome faeces
Kannan Ponnusamy, Jung Nam Choi, Jiyoung Kim, Sun-Young Lee, Choong Hwan Lee
Journal of Medical Microbiology .2011; 60(6): 817. CrossRef
Halophilic archaea in the human intestinal mucosa
Andrew P. A. Oxley, Mariana P. Lanfranconi, Dieco Würdemann, Stephan Ott, Stefan Schreiber, Terry J. McGenity, Kenneth N. Timmis, Balbina Nogales
Environmental Microbiology.2010; 12(9): 2398. CrossRef
The Discussion Goes on: What Is the Role ofEuryarchaeotain Humans?
H.-P. Horz, G. Conrads
Archaea.2010; 2010: 1. CrossRef
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Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Eun-Jin Park, Jin-Woo Bae
The ISME Journal.2010; 4(1): 1. CrossRef
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JOSEPH D. COOLON, KENNETH L. JONES, SANJEEV NARAYANAN, SAMANTHA M. WISELY
Molecular Ecology.2010; 19(s1): 67. CrossRef
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E. Perez-Rueda, S. C. Janga
Molecular Biology and Evolution.2010; 27(6): 1449. CrossRef

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