Papers by Ibrahim B B Farouk
Exploring the Genomic and Metabolic Characteristics of the Candidate Phylum Latescibacteria (candidate phylum WS3) using single-cell genomics
Single cell genomics is a promising approach for deciphering metabolic capacities, and ecological... more Single cell genomics is a promising approach for deciphering metabolic capacities, and ecological roles of yet uncultured bacterial lineages. We present a detailed analysis of four single amplified genomes (SAGs) belonging to the bacterial candidate phylum Latescibacteria (WS3), from two aquatic environments Etoliko lagoon, Greece and Sakinaw Lake, British Columbia. Latescibacteria SAGs exhibited low G+C content (42-43.5%), large genome size (estimated between 3.1 MB to 7.7 MB), and each harbored a single copy of the ribosomal RNA (rRNA) operon. Metabolic reconstruction on the combined dataset suggests a lifestyle based on the uptake and conversion of sugars, fatty acids, and amino acids as carbon sources. Specifically, the genomes encoded the capacity to degrade integral components of algal and plant cell walls including fucose, rhamnose, and sulfated sugar derivatives. The metabolism of these carbon sources is commonly associated with the production of propanediol and other toxic ...
PLOS ONE, 2015
The "Latescibacteria" (formerly WS3), member of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) su... more The "Latescibacteria" (formerly WS3), member of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the "Latescibacteria" were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed "Latescibacteria" mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed.
PLoS ONE, 2014
We investigated the global patterns of abundance, diversity, and community structure of members o... more We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ,1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as nonsaline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions.
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Papers by Ibrahim B B Farouk