Table_4_The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation.xlsx

<p>Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.</p

Table_5_The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation.xlsx

<p>Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.</p

Table_3_The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation.xlsx

<p>Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.</p

Direct Experimental Evidence of Non-first Order Degradation Kinetics and Sorption-Induced Isotopic Fractionation in a Mesoscale Aquifer: ¹³C/¹²C Analysis of a Transient Toluene Pulse

The injection of a mixed toluene and D₂O (conservative tracer) pulse into a pristine mesoscale aquifer enabled a first direct experimental comparison of contaminant-specific isotopic fractionation from sorption versus biodegradation and transverse dispersion on a relevant scale. Water samples were taken from two vertically resolved sampling ports at 4.2 m distance. Analysis of deuterium and toluene concentrations allowed quantifying the extent of sorption (<i>R</i> = 1.25) and biodegradation (37% and 44% of initial toluene at the two sampling ports). Sorption and biodegradation were found to directly affect toluene ¹³C/¹²C breakthrough curves. In particular, isotope trends demonstrated that biodegradation underwent Michaelis–Menten kinetics rather than first-order kinetics. Carbon isotope enrichment factors obtained from an optimized reactive transport model (Eckert et al., this issue) including a possible isotope fractionation of transverse dispersion were ε^equ_sorption = −0.31 ‰, ε^kin_{transverse‑dispersion} = −0.82 ‰, and ε^kin_{biodegradation} = −2.15 ‰. Extrapolation of our results to the scenario of a continuous injection predicted that (i) the bias in isotope fractionation from sorption, but not transverse dispersion, may be avoided when the plume reaches steady-state; and (ii) the relevance from both processes is expected to decrease at longer flow distances when isotope fractionation of degradation increasingly dominates