Exploring halophilic environments as a source of new antibiotics

Figures & data

Figure 1. Timeline depicting the year in which antibiotic resistance in each major class of antibiotics was first observed. The main mechanism of resistance for each antibiotic class is also included.

Figure 2. Successive generations of major antibiotic classes over time. Black bonds represent the original skeletal structure while red bonds are structural changes.

Table 1. Antimicrobial compounds from halophilic and halotolerant actinomycetes.

Source	Compound	Structure	Reference
Streptomyces sp. strain B6921 (Sediment, Mauritius Indian Ocean)	Himalomycins		(Maskey, Li, et al. 2003)
Verrucosispora sp. strain AB-18-032 (Sediment, Sea of Japan)	Abyssomicins B–D
Micromonospora sp. strain DPJ12 (Isolated from Didemnum proliferum)	Diazepinomicin		(Charan et al. 2004)
Streptomyces sp. (NA)	Gutingimycin		(Maskey et al. 2004)
Streptomyces nodosus (NPS007994) (Marine sediment, California)	Lajollamycin		(Manam et al. 2005)
Salinispora tropica, strain CNB-392 (Marine sediment, Bahamas)	Sporolides A and B		(Buchanan et al. 2005)
Salinispora pacifica CNS103 (NA)	Cyanosporasides A and B		(Oh et al. 2006)
Streptomyces sp. strain CNH365 (Marine sediment, Santa Barbara, California)	Anthracimycin		(Jang et al. 2013)
Nocardiopsis terrae YIM 90022 (NA)	Quinolone alkaloid		(Tian et al. 2014)
Streptomyces sp. strain DB634 (Atacama Desert, Chile)	Abenquines A-D		(Schulz et al. 2011)
Streptomyces sp. strain C34 (Atacama Desert, Chile)	Chaxalactins A-C		(Rateb, Houssen, Harrison 2011)
Saccharothrix sp. SA198 (Saharan soil)	Antibiotic A4 and A5		(Boubetra et al. 2013)
Streptomyces sp. TK-VL_333 (Algeria)	4-(4-hydroxyphenoxy) butan-2-one		(Kavitha et al. 2010)
Streptomyces sp. TK-VL_333 (Algeria)	Acetic acid-2-hydroxy- 6-(3-oxo-utyl)-phenyl ester		(Kavitha et al. 2010)
Streptomyces sp. C34 (Laguna de Chaxa, Salar de Atacama, Chile)	Chaxamycins A–D (1-4)		(Rateb, Houssen, Arnold 2011)

Table 2. Forward and Reverse primer sequences for Halocins S8, H4 and C8.

Halocin	Primer sequence
S8	F1 (5′-GCTTCAGCTGTCGGATTTTC-3′)
	R1 (5′-CTTCAAGTATCGCGGACACA-3′)
H4	F1 (5′-CAGTCTCGGAGCGCTTAGTT-3′)
	R1 (5′-CGGGATACTTGGGTTCTTCA-3′)
C8	C8-IG1 (5′-ACGCTGTGCGAGTAGGAGTT-3′)
	C8- IG2 (5′-GAGACGACGTTCGAGGAATC-3′)
	C8-9 (5′-CCGACGGGGTGCAGTCC-3′)
	C8-10 (5′-CGTCACCGCAACCGCTGT-3′)

Table 3. Characterisation of known halocins, with thermal stability, salt dependency, the spectrum of activity, mechanism, and known sequences.

Halocin	Source	Size (kDa)	Thermal stability	Salt-dependence	Activity spectrum^a	Mechanism	Peptide sequence	Reference
A4	Haloarchaeon strain TuA4	<5	≥1 week at boiling	No	Broad Sulfolobus spp.	ND	ND	(Haseltine et al. 2001; O’Connor and Shand 2002)
C8	Halobacterium sp. AS7092	6.3	≥1 h at boiling	No	Broad	Cell wall	H2N-DIDITGCSACKYAAGQVCTIGCSAAGGFICGLLGITIPVAGLSCLGFVEIVCTVADEYSGCGDAVAKEACNRAGLC-COOH	(Li et al. 2003; Meknaci et al. 2014)
G1	Halobacterium strain GRB	ND	ND	ND	Broad	ND	ND	(Soppa and Oesterhelt 1989)
HA1	Haloferax larsenii HA1	∼14	<80 °C	Yes	Narrow	Rupturing cell boundary	ND	(Kumar and Tiwari 2017b)
HA3	Haloferax larsenii HA3	∼13	<80 °C	Gradual reduction at 4 °C	Narrow	Rupturing cell boundary	ND	(Kumar and Tiwari 2017a)
H1	Haloferax mediterranei Xai3	31	<50 °C	Yes	Broad	Membrane permeability	ND	(Rodriguez-Valera et al. 1982; Platas et al. 1996)
H2	Haloarchaeon strain GLA22	ND	ND	ND	Broad	ND	ND	(Rodriguez-Valera et al. 1982)
H3	Haloarchaeon strain GAA12	ND	ND	ND	Broad	ND	ND	(Rodriguez-Valera et al. 1982)
H4	Haloferax mediterranei R4	39.6 preprotein	<60 °C	Partially	Narrow	Proton flux	H2N-MSKDRDGRRTSRRGTLKKIGGFSLGALSFGAVGRTQAATGSSVTTADIAPPGPNGDPKSVQIDDKYTGAEMYGEGDFRVGLGTDLTMYPPVYRESLGNGSGGWEFDFTVCGSTACRFVDSNGDVKEDDKAKEMWWQEINFNDINQDLYSRNDSDWVGSTPADTQPEFDYTDFALARDGVTLALTALNPAMGSLALGATYFLSDMVNWIASQHEDDSSLKRKWDYDGLSGPLYADSSTYLLARDEMTSNSYESFTIDNIAVAFPEFPVRTKYYVTFTAPDDPSTQSISTLEEEGIYRVPATEVAAARPPGSRRSKSAADEMVYVADPKKFIEVEPVKNPSIPDRIYEEIEQKKKQRSRKQ-COOH	(Rodriguez-Valera et al. 1982; Meseguer and Rodriguez-Valera 1985, 1986; Meseguer et al. 1995; Cheung et al. 1997; Shand et al. 1999)
H5	Haloarchaeon strain MA220	ND	ND	ND	Narrow	ND	ND	(Rodriguez-Valera et al. 1982)
H6/H7	Haloferax gibbonsii Ma2.39	32	≤90 °C	No	Broad Sulfolobus spp. M. thermaphila	Na^+/H^+ antiporter inhibitor	ND	(Rodriguez-Valera et al. 1982; Torreblanca et al. 1989; Meseguer et al. 1995)
H17	Haloferax sp. SWI17	30–40	ND	ND	Halobacterium salinarum DSM3754	ND	ND	(Mazguene et al. 2018)
KPS1	Haloferax volcanii KPS1	ND	<80 °C	Yes	Broad E. coli, S. mutans, P. aeruginosa, B. subtilis, S. aureus	ND	ND	(Kavitha et al. 2011)
R1	Halobacterium sp. GN101	3.8	60 °C	No	Broad	ND	N2H- LQSNININTAAAVILIFNQVQVGALCAPTPVSGGGPPP-COOH	(Shand et al. 1998; Haseltine et al. 2001; O’Connor and Shand 2002)
Sech7a	Haloferax erranei AY823953	10.7	<80 °C	Yes	ND	Potentially novel	ND	(Pašić et al. 2008)
SH10	Natrinema sp. BTSH10	ND	ND	ND	ND	Cellular swelling	ND	(Pašić et al. 2008)
S8	Haloarchaeon Strain S8a	3.6 mature	≥24 h at boiling	No	Broad Sulfolobus spp.	ND	H2N-SDCNINSNTAADVILCFNQVGSCALCSPTLVGGPVP-COOH.	(Shand et al. 1999; Price and Shand 2000; Haseltine et al. 2001)

^aActivity spectrum refers to inhibition of haloarchaea unless otherwise indicated. ND: not determined.

Table 4. Examples of QSI compounds and their corresponding activity produced from halophilic and halotolerant bacteria.

Source	Compound	Structure	Activity	Reference
Halobacillus salinus C42	N-(2′-phenylethyl)-isobutyramide		Inhibition of bioluminescence by V. harveyi BB120 Inhibition violacein production against Chromobacterium violaceum CV026	(Teasdale et al. 2009)
	2,3-methyl-N-(2′-phenylethyl)-butyramide		Inhibition of bioluminescence by V. harveyi BB120 Inhibition of violacein production against C. violaceum CV026 Inhibition of violacein production against C. violaceum ATCC 12472 Inhibition of green fluorescence protein by E. coli JB525
Bacillus cereus D28	Cyclo (L-Pro-L-Try)		Inhibition of bioluminescence by V. harveyi BB120 Inhibition of violacein production against C. violaceum ATCC 12472	(Teasdale et al. 2011)
Marinobacter sp. SK-3	Cyclo (L-Pro-L-Phe)		Inhibition of bioluminescence production in E. coli pSB401	(Abed et al. 2013)
	Cyclo (L-Pro-L-Leu)		Inhibition of bioluminescence production in E. coli pSB401 Inhibition of QS violacein production by C. violaceum CV-017
	Cyclo (L-Pro-L isoLeu)		Inhibition of bioluminescence production in E. coli pSB401 Inhibition of QS violacein production by C. violaceum CV-017
Blennothrix antharidosmum	Tumonoic acid F		Inhibition of bioluminescence by V. harveyi BB120	(Clark et al. 2008)
Lyngbya majuscula	Malyngolide		Inhibition of violacein production against C. violaceum CV017 Las QS-dependent production of elastase by P. aeruginosa PAO1.	(Dobretsov et al. 2010)
Leptolyngbya crossbyana	Honaucin A Honaucin B Honaucin C		Inhibition of bioluminescence by V. harveyi BB120	(Choi et al. 2012)

Table 5. Structures of antimicrobials identified through genome mining from five species of bacteria.

Source	Compound	Structure	Reference
Pseudomonas fluorescens Pf-5	Orfamide A		(Gross 2007)
Streptomyces tropica CNB-440	Salinilactam A		(Udwary et al. 2007)
Streptomyces clavuligerus ATCC 27064	Holomycin		(Li and Walsh 2010)
Aspergillus nidulans R153	Emericellamide A, C–E		(Chiang et al. 2008)
Haliangium ochraceum SMP-2	Haliamide		(Sun et al. 2016)

Figure 3. Summary describing the two main approaches that used for antimicrobial discovery from metagenomes. Adapted from Hug et al. (2018).

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