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| Hassan,Mariam; Essam,Tamer; Megahed,Salwa. |
| Abstract In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree)... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Bioinformatics; Method; Microbiome; Next-generation sequencing; QIIME. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000500001 |
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| Dubé, Caroline; Ky, Chin-long; Planes, Serge. |
| Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland,... |
| Tipo: Text |
Palavras-chave: Pearl oyster; Microbiome; Tissue-specific bacterial communities; 16S rRNA gene sequencing; Functional profiling prediction. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00505/61670/65589.pdf |
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| Clerissi, Camille; De Lorgeril, Julien; Petton, Bruno; Lucasson, Aude; Escoubas, Jean Michel; Gueguen, Yannick; Dégremont, Lionel; Mitta, Guillaume; Toulza, Eve. |
| Pacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and causes important economic losses. Disease dynamic was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 μVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to protect oysters against POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favor of POMS. After 5 days of transplantation, oysters from... |
| Tipo: Text |
Palavras-chave: Holobiont; Microbiome; Metabarcoding; Fitness; Bacteria. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00621/73332/72500.pdf |
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| Souza,Renata Carolini; Cantão,Maurício Egídio; Nogueira,Marco Antonio; Vasconcelos,Ana Tereza Ribeiro; Hungria,Mariangela. |
| ABSTRACT The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases > laccases > cellulases > proteases > amylases > pectinases. Statistically significant differences were attributed to the... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Metagenome; Microbiome; Soil enzymes; Soil management; No-tillage. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000400723 |
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| Clauss,Marcus; Hummel,Jürgen. |
| ABSTRACT Herbivores face the dilemma that the level of feed intake is negatively related to factors that determine digestive efficiency, such as thoroughness of ingesta comminution by chewing, and retention of digesta in the digestive tract. Ruminants have evolved particular adaptations to solve this dilemma. Most ruminants share the characteristic of “digesta washing”: fluid moves through their digestive tract faster than particles, thus effectively washing very fine particles, such as bacteria, out of the digesta plug. As the forestomach is followed by auto-enzymatic digestion, this allows a continuous, increased harvest of microbes from the forestomach. True rumination only evolved twice, in the camelids and the true ruminants. These both evolved a... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Cattle; Digesta washing; Foregut fermenter; Microbial harvest; Microbiome. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982017000700606 |
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| BOTERO,Luz Elena; DELGADO-SERRANO,Luisa; CEPEDA HERNÁNDEZ,Martha Lucía; DEL PORTILLO OBANDO,Patricia; ZAMBRANO EDER,María Mercedes. |
| During the last decade, there has been increasing awareness of the massive number of microorganisms, collectively known as the human microbiota, that are associated with humans. This microbiota outnumbers the host cells by approximately a factor of ten and contains a large repertoire of microbial genome-encoded metabolic processes. The diverse human microbiota and its associated metabolic potential can provide the host with novel functions that can influence host health and disease status in ways that still need to be analyzed. The microbiota varies with age, with features that depend on the body site, host lifestyle and health status. The challenge is therefore to identify and characterize these microbial communities and use this information to learn how... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: 16S rRNA gene; Microbial diversity; Microbiome; Mycobacterium tuberculosis. |
| Ano: 2016 |
URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-548X2016000100001 |
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| Colonetti,Karina; Roesch,Luiz Fernando; Schwartz,Ida Vanessa Doederlein. |
| Abstract Research into the influence of the microbiome on the human body has been shedding new light on diseases long known to be multifactorial, such as obesity, mood disorders, autism, and inflammatory bowel disease. Although inborn errors of metabolism (IEMs) are monogenic diseases, genotype alone is not enough to explain the wide phenotypic variability observed in patients with these conditions. Genetics and diet exert a strong influence on the microbiome, and diet is used (alone or as an adjuvant) in the treatment of many IEMs. This review will describe how the effects of the microbiome on the host can interfere with IEM phenotypes through interactions with organs such as the liver and brain, two of the structures most commonly affected by IEMs. The... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Inborn errors of metabolism; Microbiome; Microbiota; Diet; Treatment. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000400515 |
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| Clerissi, Camille; Guillou, Laure; Escoubas, Jean Michel; Toulza, Eve. |
| Background Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. Results To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities... |
| Tipo: Text |
Palavras-chave: Holobiont; Metabarcoding; Microbiome; Ostreoida; Crassostrea. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00636/74799/75165.pdf |
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