Table 3.
Some novel antimicrobials, anti-infectives and antimicrobial resistance genes discovered through functional metagenomics.
| Antimicrobial | Closest known relationship (percentage homology) | Method/Host | Environment | References |
|---|---|---|---|---|
| Long-chain N-acyltyrosine synthase genes | No identity to bacteria cultured at that time. Some similarity to predicted proteins from Nitrosomonas europaea, Desulfovibrio vulgaris, and D. desulfuricans | Activity-based screening of E. coli cosmid library | Seven soil samples, Ithaca, NY Boston, MA Costa Rica | Brady et al., 2004 |
| N-acyl amino acid biosynthesis gene | Highest similarity to hypothetical protein (MJ1207) from Methanococcus jannaschii | Activity-based screening of E. coli cosmid library | Soil | Brady and Clardy, 2000 |
| Two isocyanide biosynthetic genes encoding isocyanide-containing antibiotic | Not available. Some identity to known and predicted proteins | Activity -based screening of E. coli cosmid library | Soil, Boston, MA | Brady and Clardy, 2005 |
| Violacein biosynthetic gene cluster | Moderate identity to Chromobacterium violaceum | Activity -based screening of E. coli cosmid library | Soil, Ithaca, NY | Brady et al., 2001 |
| Two ORFs within a clone encoding a transcriptional regulatory protein and a putative indole oxygenase | The indole oxygenase-like protein showed high identity to naphthocyclinone hydroxylase (NcnH) from Streptomyces arenae | Activity -based screening of E. coli fosmid library | Forest topsoil, Jindong Valley, Korea | Lim et al., 2005 |
| Turbomycin A, B | The ORFs encoding the turbomycins A and B show 53% identity to legiolysin from Legionella pneumophila, 54% identity to hemolysin from Vibrio vulnificus, 49% identity to 4-hydroxyphenylpyruvate dioxygenase from Pseudomonas and 45% identity to MelA in Shewanella colwelliana | Activity-based screening of E. coli plasmid library | Soil | Gillespie et al., 2002 |
| Uncharacterized protein with antimicrobial activity | Low to moderate sequence identity (26–58%) to proteins and hypothetical proteins from Solitalea canadensis DSM 3403 (38 and 46%), Flavobacterium sp. CF136 (26%), Indibacter alkaliphilus LW1 (40%), Helicobacter bizzozeronii CIII-1 (31%) and Acidovorax sp. JS42 (58%) | Activity-based screening of E. coli-Bacillus subtilis shuttle vector library | Soil sample from a deciduous forest, Belgium | Biver et al., 2013b |
| Novel chitinase with chitobiosidase activity (identified by the sequence-based approach) | 45% identity to chitinase from an uncultured bacterium (Uchiyama and Watanabe, 2006) and amino acid identity to known proteins from Chondromyces apiculatus (41%), Corallococcus coralloides (40%), and Myxococcus xanthus (39%) | Targeted sequence-based analysis and activity-based screening of E. coli fosmid library | Soil, Swedish University of Agricultural Sciences, Uppsala, Sweden | Hjort et al., 2014 |
| Six clones with antimicrobial activity: two with cell wall-degrading activity, three proteases and a lipolytic enzyme | 54–31% identity to known amidase, lytic transglycosylase and proteases from Desulfovibrio sp. U5L, Clostridium sp. CAG:1013, Myxococcus xanthus, Leptospira santarosai and Ferroglobus placidus and to a putative lipolytic enzyme from an uncultured bacterium | Activity-based screening of broad-host cosmid shuttle vector library expressed in Ralstonia metallidurans | Soil, Sonoran Desert, Arizona, USA | Iqbal et al., 2014 |
| Six clones encoding a lysostaphin gene | All six clones expressed the lysostaphin gene from the Staphylococcus simulans library strain | High throughput activity-based screening of E. coli and Saccharomyces cerevisiae plasmid libraries | Library derived from three native staphylococcal strains: S. simulans, S. arlettae, and S. equorum | Scanlon et al., 2014 |
| ANTI INFECTIVE | ||||
| Two novel lactonases | One had 53% similarity to amino acid sequence from Pseudomonas fluorescens. The other, 57% similarity to Nitrobacter sp. Strain Nb-311A | Activity-based screening of E. coli phagemid vector, plasmid and broad-host-range vector library | Soil, University of Göttingen, Germany | Schipper et al., 2009 |
| Clone expressing NAHL-lactonase activity | Most closely related to Zn-dependent hydrolase from Bradyrhizobium sp. | Functional-based screening of E. coli fosmid library | Pasture soil, France | Riaz et al., 2008 |
| Two novel pairs of LuxR/LuxI genes | QS pair 1: LuxI homolog: 42% amino acid similarity to putative LuxI in Geobacter uraniireducens Rf4. 38% protein sequence similarity to CviI in Chromobacterium violaceum ATCC 31532. LuxR homolog: 33% amino acid similarity to LuxR from Geobacter sp. strain FRC-32 and 31% to CviR from C. violaceum QS pair 2: LuxI homolog: 57% similar to LuxIQS6-1 of a metagenomic clone and 40% amino acid similarity to PpuI from Pseudomonas putida. LuxR homolog: 37% similarity to LuxRQS10-1 in a metagenomic clone and 35% similarity to BraR in Burkholderia kururiensis | Activity-based screening of two fosmid libraries expressed in a biosensor E. coli host | Activated sludge from a coke plant, Japan. Forest soil samples, Tsukuba city, Japan | Nasuno et al., 2012 |
| Novel bacterial NAHLase | Most likely belonging to species of unknown Proteobacterium | Activity-based screening using an Agrobacterium tumefaciens biosensor strain of four E. coli fosmid libraries | Rhizosphere of Solanum tuberosum that was treated with γ-caprolactone | Tannieres et al., 2013 |
| Three novel pair of LuxR/LuxI genes | QS pair 1: 47% identity to Nitrosospira multiformis ATCC 25196 and 34% to Nitrococcus mobilis Nb-231 QS pair 2: 51% and 32% identity to Nitrosospira multiformis ATCC 25196 QS pair 3: both genes had 37% identity to proteins from Sphingomonas sp. SKA58 | Activity-based screening using an Agrobacterium tumefaciens biosensor strain of four E. coli plasmid libraries | Activated sludge Soil | Hao et al., 2010 |
| Novel NADP-dependent short-chain dehydrogenase/reductase | 61% identical to chromosome segregation protein SMC in Acidobacterium sp. MP5ACTX8 | Activity-based screening of E. coli phagemid vector, plasmid, and broad-host-range vector library | Soil, University of Göttingen, Germany | Bijtenhoorn et al., 2011 |
| ANTIBIOTIC RESISTANCE DETERMINANT | ||||
| Novel florfenicol and chloramphenicol resistance gene | 33% amino acid identity to drug resistance transporters from Wolbachia spp. (YP_002726856, YP_198189, and NP_966057) | Function-based screening of E. coli fosmid library | Soil samples from an island in the Tanana River near Fairbanks, Alaska | Lang et al., 2010 |
| Two novel genes conferring resistance to kanamycin and ceftazidime | Both showed highest similarity to uncultured soil microorganisms | Activity-based screening of E. coli fosmid library | Soil from apple orchard, southern Wisconsin | Donato et al., 2010 |
| Resistance genes to chloramphenicol, ampicillin and kanamycin. Multidrug resistant clone conferring ampicillin and kanamycin resistance | Multidrug resistant clone showed highest identity (95%) to a ß-lactamase from Bacillus sp. BT-192. For chloramphenicol resistance, highest homology was seen to a hypothetical protein from Methylibium petroleiphilum. A kanamycin resistant clone showed 55% identity to a Microscilla sp. protein. An ampicillin resistant clone showed 66% identity to a ß-lactamase from Spirosoma linguale | Functional screening of metagenomic BAC, plasmid, and phagemid vector libraries expressed in E. coli. Sequencing of small insert libraries. | Activated sludge | Parsley et al., 2010 |
| Novel chloramphenicol hydrolase (resistance to chloramphenicol and florfenicol) | 14 ORFs varying in similarity (30–77%) to corresponding proteins from known microorganisms. Highest similarity overall to proteins from the bacterial phylum Proteobacteria | Activity-based screening of E. coli plasmid library | Alluvial soil | Tao et al., 2012 |
| Novel carboxylesterase | Highest identity (58%) to ß-lactamase (YP_004154831) from Variovorax paradoxus EPS | Activity-based screening of E. coli cosmid library | Soil from the Upo wetland, South Korea | Jeon et al., 2011 |
| 31 previously undescribed antibiotic resistance genes to ampicillin, amoxicillin, tetracycline, and penicillin. This includes class A and C β-lactamases and six different tetracycline resistance genes | Significant similarity to proteins from multiple genera from the ARDB and GenBank databases | Activity-based screening of E. coli plasmid library | Fecal samples of Herring gulsl, Appledore Island, ME and Rochester, NH, USA | Martiny et al., 2011 |
| 39 clones conferring resistance to kanamycin, gentamicin, chloramphenicol, rifampin, trimethoprim, and tetracycline | Highest homology to the following phyla: Proteobacteria, Actinobacteria, and Firmicutes | Activity-based screening of E. coli plasmid library | Urban soil, Seattle, WA, USA | McGarvey et al., 2012 |
| 110 antibiotic resistance genes conferring resistance to ß-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines, including 55 ß-lactamases | 18 resistance genes showed 100% identity to known human pathogens | Activity-based screening of metagenomic library expressed in E. coli coupled with PARFuMS | 11 soil samples, USA | Forsberg et al., 2012 |
| 95 unique antimicrobial resistance eDNA inserts. 10 novel β-lactamase gene families | Average of 69.5% nucleotide identity to GenBank sequences. 15 β-lactamase resistance genes showed high identity (>90%) to known human pathogens | Activity-based screening of metagenomic library expressed in E. coli | Human saliva and fecal samples | Sommer et al., 2009 |
| A novel kanamycin resistance gene fusion (to a hypothetical protein domain) | N-terminus was 42% identical to AAC(6') from Enterococcus hirae. C-terminus was 35% identical to a hypothetical protein (CBL37632) from Clostridiales sp. SSC/2 | Activity-based screening of E. coli fosmid library | Four human fecal samples | Cheng et al., 2012c |
| 45 clones resistant to tetracycline, minocycline, aminoglycosides, streptomycin, gentamicin, kanamycin, amikacin, chloramphenicol, and rifampicin | 26–92% similarity to known proteins in the GenBank database | Activity-based screening of E. coli plasmid library | Four agricultural soil samples, China | Su et al., 2014 |
| Five clones conferring Fluoroquinolone resistance, cephalosporin resistance, and trimethoprim resistance | High similarity to homologs in species of Bacillus, Erwinia, Exiguobacterium, Pseudomonas | Activity-based screening of two E. coli plasmid libraries from cultured spinach microbiota and from uncultured spinach wash | Retail spinach | Berman and Riley, 2013 |
| Ampicillin resistance and kanamycin resistance | Homology to Streptococcus thermophilus and Lactobacillus helveticus | Activity-based screening of an E. coli fosmid library | Mozzarella di Bufala Campana (MBC) Cheese, produced in Central and Southern Itlaly | Devirgiliis et al., 2014 |