1 Supplementary Notes
2
3 Supplementary Note 1. Functional characterization
4 Facial and gut microbiomes comparisons
5 We also identified 2 genes from lipid metabolism, 2 genes to glycan biosynthesis, and metabolism
6 and peptidoglycan biosynthesis, and 1 gene present only the face dataset related to
7 phenylpropanoid biosynthesis from Alistipes (related to protection from UV light, and defence
8 against herbivores and pathogens [1–3]). Interestingly, ~98x more bacteria in the face microbiome
9 is annotated as moderate halophilic (face= 11,239, gut= 115), as well as ~239 times more
10 psychrophilic bacteria in the face (face= 18,886, gut= 79). The top 5% with the largest difference
11 in abundance from the pathways that drive variation between the face and gut microbiomes,
12 contains the metabolism of fructose and mannose, starch and sucrose, galactose, and amino sugar
13 and nucleotide sugar, all of them more abundant in the gut microbiome.
14
15 Microbial cores
16 Besides the defined microbial taxonomic and functional cores obtained from the MGmapper
17 results (Additional File 11), we defined other types of cores based on the taxonomies assigned to
18 the annotated genes. The percentage of annotated genes in the face dataset has a median of 72.61%
19 (mean of 57.8%), and a median of the gut dataset is 66.75% (mean of 65.08%). From the nr gene
20 catalogue we defined 2 types of cores. A strict core, in which we keep those genes present in a
21 given minimum number of samples taking the taxa from where the genes derive into account
22 (Table S5). The second type of core, a relaxed one, does not take taxonomy of the genes into
23 account, and keeps those genes present in a given minimum number of samples (Table S6).
1 24 Looking at the taxonomic identifications from the protein annotations, we found 12 virus taxa in
25 all the face samples, 7 fungi, and 26 bacterial strains. In the gut samples, we found 9 bacterial
26 strains, 11 fungi, and 18 viruses.
27
28 Cadaverine and putrescine: Three of the main molecules produced in a decomposing body are
29 nitrate reductase (converting nitrite to ammonia) [4], cadaverine (lysine decarboxylase) [5], and
30 putrescine (ornithine decarboxylase) [5] (Additional File 5). In this regard, we identified in the
31 face MOCAT nr strict core a spermidine synthase gene from Janthinobacterium sp. HH01, and
32 spermidine/putrescine ABC transporter ATPase in both face and gut MOCAT strict cores from
33 Herbaspirillum sp. GW103. Sulphur compounds are also emitted by decomposing carcasses [6],
34 likely derived from methionine and cysteine degradation. This likely explains the identification of
35 the metabolism of cysteine and methionine as the two most abundant subclasses from the amino
36 acids metabolism in both face and gut microbiomes. A carcass also produces volatile organic
37 compounds [7], such as acetone, methyl ethyl ketone, toluene, ethylbenzene, m,p-xylene, styrene,
38 and o-xylene. In this regard, toluene degradation is one of the subclasses not driving variation in
39 the face functional intra samples comparison, and the MOCAT face cores have more genes related
40 to xenobiotics biodegradation metabolism than those of the gut microbiome (Additional File 5).
41
42 Supplementary Note 2. Microbiome cores identifications
43 Core microbiome identification: In the filtered MGmapper taxonomic profiling, we identified
44 1,483 species in the facial samples, 638 of which are in at least 50% of the samples (relaxed core),
45 and only 184 in at least 80% of the samples (strict core). In the gut microbiome we found 1,419
46 microbial species, with only 322 present in at least 50% of the samples, and 129 in at least 80%.
2 47 In the functional characterization we identified a total of 238,065 nr unique bacterial genes in the
48 face microbiome and 387,951 nr unique bacterial genes in the gut microbiome (Additional File 4,
49 Tables S4, S5). Besides the defined microbial taxonomic and functional cores obtained from the
50 MGmapper results (Additional File 11), we defined other types of cores based on the taxonomies
51 assigned to the annotated genes. The percentage of annotated genes in the face dataset has a median
52 of 72.61% (mean of 57.8%), and a median of the gut dataset is 66.75% (mean of 65.08%). From
53 the nr gene catalogue we defined 2 types of cores. A strict core, in which we keep those genes
54 present in a given minimum number of samples taking the taxa from where the genes derive into
55 account (Table S5). The second type of core, a relaxed one, does not take taxonomy of the genes
56 into account, and keeps those genes present in a given minimum number of samples (Table S6).
57 Looking at the taxonomic identifications from the protein annotations, we found 12 virus taxa in
58 all the face samples, 7 fungi, and 26 bacterial strains. In the gut samples we found 9 bacterial
59 strains, 11 fungi, and 18 viruses.
60
61 Supplementary Note 3. Digestive role of the gut microbiome
62 Intestinal microbiome related to digestion: Among the taxa present in higher abundance in the
63 face microbiome than in the gut microbiome, we identified taxa and functions that are usually part
64 of the gut microbiome of mammals (Additional File 3). These bacteria could be derived from the
65 carrion but be removed from the vulture gut microbiome. For example, present only in the face
66 dataset is Cellulophaga lytica, which is capable of degrading proteins and polysaccharides [8], as
67 well as Flavobacterium columnare, which produces gelatin-degrading and chondroitin sulfate-
68 degrading enzymes [9,10]. This is relevant given that chondroitin sulfate is one of the main
69 structural components of cartilage. Although we did not identify these genes from F. columnare,
3 70 we identified chondroitin sulfate ABC lyase genes in both face (4 genes from Bacteroides and
71 Proteus) and gut microbiomes (13 genes from Bacteroides, Edwardsiella, and Proteus).
72
73 Fusobacterium digestive roles: It has been proposed that the abundance of Fusobacterium in the
74 gut could aid in the digestion of meat, given their ability to metabolize amino acids [11,12]. This
75 suggestion is supported by the finding of F. nucleatum and F. varium in the vulture’s gut
76 microbiome. One of the most abundant genes in the gut microbiome is an alpha-2-macroglobulin
77 family protein from F. mortiferum (the most abundant Fusobacterium in the gut), this protein has
78 been suggested to be used in bacteria as a colonization rather than a virulence factor [13]. Besides,
79 eukaryotic alpha-2-macroglobulin, produced by the liver, binds to and removes MMP-2 and MMP-
80 9 (active forms of the gelatinase), which is produced in the stomach to digest gelatin [13,14].
81 However, gelatin’s colloidal properties aid in the digestion of various types of food [15,16].
82 Furthermore, bacterial alpha-2-macroglobulin can be structurally very similar to that of eukaryotes
83 [17]. This suggests that Fusobacterium could also be playing digestive aiding roles in the vulture
84 gut.
85
86 Supplementary Note 4. Taxonomic characterization
87 Pathogenic characterization: Looking at the identified bacteria taking into account the strain
88 information (Additional File 12), the maximum number of potentially pathogenic bacteria
89 identified in a sample (a face sample) was 482, and the minimum was 10, with a mean of 159.8.
90 Each pathogen was present in a mean number of 11.98, a minimum of 1, and a maximum of 75
91 (Clostridium perfringens ATCC 13124 and Clostridium perfringens str. 13). We found that the
92 face has more different species of potential pathogens than the gut (P= 0.036, face mean= 189.79,
4 93 gut mean= 137.29). Present in at least 90% of the samples are three Clostridium perfringens strains
94 which produce gas gangrene [18], and one Stenotrophomonas maltophilia, which produces
95 bacteremia, bronchitis, pneumonia, and urinary tract infection [19]. In the gut samples, the most
96 abundant hosts for the potentially pathogenic bacteria are human, chicken, turkey, cattle, pigs, and
97 mouse. For those in the face, the most abundant hosts are human, followed by cattle, and plants.
98 Among the 19 potentially pathogenic bacteria present only in the gut samples are Brachyspira
99 pilosicoli, Campylobacter coli and Campylobacter jejuni strains, some strains of C. difficile and
100 E. coli, Salmonella enterica strains, and some Shigellas (S. boydii, S. dysenteriae, and S. flexneri).
101 And among those 50 present only in the face dataset, we found various strains of Acinetobacter
102 baumannii, Actinobacillus pleuropneumoniae, Burkholderia, Capnocytophaga gingivalis ATCC
103 33624, some Vibrio species (V. harveyi HY01, V. ordalii ATCC 33509, V. shilonii AK1, V.
104 splendidus 12B01, and V. tasmaniensis ZS-17), various Xanthomonas, among others (Table 2).
105
106 Fusobacteria and Clostridia pathogenicity: It has been speculated that the large amount of
107 Fusobacteria and Clostridia in the vulture gut outcompetes other more virulent and toxic relatives,
108 being harmless pathogenic versions that occupy the space and resources that more pathogenic
109 versions would occupy otherwise, thus serving as a sort of probiotics [20]. To examine this
110 hypothesis, we searched for toxin-related genes from these taxa in the gut functional core. We
111 identified two putative enterotoxins from C. perfringes, and interestingly, also a protein in two gut
112 samples from the bacteriocinogenic plasmid pIP404 from C. perfringes [21]; less toxin-related
113 genes were found for Fusobacterium (Additional Files 9, 10).
114
5 115 Supplementary Note 5. Microbiome mediated protection
116 Probiotics and beneficial functions: One of the most abundant taxa in the face microbiome is
117 Pseudomonas fluorescens, which can produce the antibiotic mupirocin [22]. This antibiotic is used
118 for treating skin, ear, and eye disorders by interfering with isoleucyl-tRNA synthetase activity of
119 pathogens, suggesting it may play a role in treating illnesses that some bacteria could cause on the
120 vulture. Among the potentially health-beneficial bacteria identified in higher abundance in the face
121 microbiome is Arthrobacter phenanthrenivorans (max. coverage in the facial samples= 4.4%,
122 max. coverage in the gut samples= 0.4%, with 163 annotated genes in the face and 66 annotated
123 genes in the gut), which is able to degrade phenanthrene [23], a skin-irritating poly-cyclic aromatic
124 hydrocarbon. Also, part of the facial functional core that takes taxonomy into account is
125 Hylemonella gracilis (max. coverage= ~4%, 69 assembled genes), which has been shown to
126 prevent long term colonization by Yersinia pestis [24]. Among the plasmids present only or most
127 abundantly in the gut microbiome, we identified those of probiotic bacteria Lactobacillus brevis
128 KB290 [25], L. casei W56 [26], L. paracasei [27], L. salivarius CECT 5713 [28], an L. reuteri
129 SD2112 [29], which produces the antimicrobial reuterin [30]. We also identified plasmids from
130 Lactobacillus sakei (max. coverage in the gut samples= 91.5%, max. coverage in the face samples=
131 26.85%), from which we also identified a putative bacteriocin immunity protein and a type II
132 secretion system protein coding gene in the nr gene catalogue. Folate has been related to skin
133 cancer prevention [31]. Notably, one of the most abundant sub-pathways in the face intra-sample
134 comparison was the folate biosynthesis. In this regard, we also identified the gene dihydropteroate
135 synthase type-2 from Acinetobacter sp. NIPH 899 in the facial microbiome. Furthermore,
136 aminobenzoate is used to treat skin disorders, and we found that the aminobenzoate degradation
6 137 subclass from the xenobiotics degradation metabolism is the most abundant in both face and gut
138 microbiomes.
139
140 Antibiotics: We identified several genes for the biosynthesis of antibiotics. Among the most
141 abundant metabolic subclasses in both face and gut microbiomes is the biosynthesis of
142 carbapenem. From the metabolism of terpenoids and polyketides, the most abundant subclasses in
143 the face and gut microbiome are the biosynthesis of tetracycline, macrolides, and ansamycins.
144 Also, among those subclasses not driving functional variation in the face microbiome are the
145 biosynthesis of monobactam, anthocyanin, and ansamycins. Furthermore, in the face MOCAT
146 strict core, we identified a gene involved in the production of naphthocyclinones antibiotics [32]
147 from Herbaspirillum frisingense [33].
148
149 Phages: In accordance to a potential phage therapy strategy, among the phages present only in the
150 face microbiome we identified the phage phi MR11, which eliminates multidrug resistant
151 Staphylococcus aureus [34]. Also Acinetobacter phage Petty, which infects Acinetobacter
152 baumanii [35], a multidrug resistant pathogen usually isolated from wounds and also identified in
153 our datasets. The phage Acibel004, active against A. baumanii [36], is also present only in the face
154 microbiome. From the face functional strict core, the most abundant phage is BPP-1, which infects
155 pathogenic Bordetella bacteria [37]. Among the identifications is the Enterobacteria phage P22
156 present only in the gut samples, infects the pathogenic S. typhimurium [38], which we also detected
157 in the gut microbiome. Furthermore, we identified the phage L-413C, which is specific for Yersinia
158 pestis [39] and identified as more abundant in the gut samples. Also present is the phage phi
159 CD119, which reduces toxin production in C. difficile [40]; notably, we also identified genes
7 160 related to C. difficile virulence. Also, the Enterobacteria phage HK620 was identified as more
161 abundant in the gut microbiome, this phage absorbs the O-antigen of E. coli H [41]. The gut
162 functional strict core contains the phage phiCD6356, which infects C. difficile [42], and phage
163 SPN3US, which has shown effective inhibition of Salmonella enterica [43]. Notably, we identified
164 putative virulent genes from S. enterica in the gut microbiome (Additional File 8).
165
166 Defense versus eukaryotes: Besides bacterial killing strategies, we also identified insecticide,
167 fungicide, and antiparasitic related taxa and genes. Among those taxa significantly more abundant
168 in the face microbiome we identified Lysinibacillus sphaericus, which produces insecticidal toxins
169 that control mosquito growth [44], and for which we assembled the gene coding for sphaericolysin,
170 an insecticidal pore-forming toxin. We also identified Pseudomonas entomophila (8 genes in the
171 gut samples, max. coverage in the gut samples= 0.2%, max. mapping reads in the gut samples=
172 216; 175 genes in the face samples, max. coverage in the face samples= 0.5%, max. mapping reads
173 in the face samples= 542) which infects insects causing lethality in fly larvae and adults [45,46]
174 and for which we identified in the nr gene set catalogue an insecticidal toxin SepC/Tcc class. We
175 also identified Streptomyces violaceusniger (present in 20 face samples, 0.1% max. coverage, 214
176 max mapping reads, 28 assembled genes; 11 gut samples, 0.03% max. coverage, 58 max mapping
177 reads, 15 assembled genes), which is an antifungal for various plant fungal pathogens [47,48].
178 Among the antiparasitic taxa in the face relaxed core, we identified Kitasatospora setae, which is
179 capable of producing the antitrichomonal setamycin [49], and Streptomyces bingchenggensis,
180 which produces the anthelmintic macrolide milbemycin [50]. We also identified Heterorhabditis
181 bacteriophora (found in 34 gut samples and 24 face samples), which kills pests like fleas, ants,
182 and flies by releasing Photorhabdus luminescens bacteria from their digestive tract [51].
8 183 Interestingly, we also identified this Photorhabdus bacteria (max. mapping reads in the gut
184 samples= 462, max. mapping reads in the face= 20). Although present in low amounts, we also
185 identified in 21 of the gut samples the Dictyostelium genera (D. intermedium and D. citrium, max.
186 mapping reads in the gut samples= 596, max. mapping reads in the face samples= 36), which is a
187 bacteriovorous protozoa present in the soil, where they keep bacterial populations in balance [52].
188 We also identified Adineta vaga, which feeds on dead organic matter, mainly dead bacteria and
189 protozoans [53] in 93.6% of the intestinal samples and 54.5% of the facial samples (gut normalized
190 abundance= 54,230, face normalized abundance= 7,972).
191
192 Non-antibiotic mechanisms: Among the taxa more abundant in the face microbiome, it is
193 interesting to note the identification of bacteria capable of growing in cancerigenous substances
194 and producers of anti-cancer immunosuppressant substances. This is of relevance given that such
195 bacteria might produce antimicrobial alternatives or products beneficial to the vulture to aid in
196 fighting the constant aggression of the toxins present in the carcasses. Present in the relaxed face
197 core we identified Chromobacterium violaceum [54] and Janthinobacterium sp. HH01 [55], which
198 produce violacein, an anticancer, antibacterial, antifungal, and antiviral compound.
199 Janthinobacterium sp. HH01 is also present in the face functional strict core. The bacteria
200 Polaromonas naphthalenivorans, capable of degrading the potentially carcinogenic naphthalene
201 [56], was present more abundantly in the face microbiome (max. mapping reads in face samples=
202 3,194, max. mapping reads gut samples= 60). This is of relevance given that 1-methyl naphthalene
203 is produced in carrion decomposition [57,58].
204
9 205 Biosurfactants represent a strong antimicrobial means of blind killing, including bacteria with
206 antibiotic resistance that would otherwise be difficult to treat. Interestingly, we identified the
207 biosurfactant producer fungi Yarrowia lipolytica [59], and the bacteria Rhodococcus erythropolis
208 [60] in both face and gut microbiomes. We also identified surfactin biosynthesis regulatory
209 proteins from Flavobacteriaceae. Furthermore, annotation of the non-mapping reads with
210 DIAMOND identified various surfactin synthetase proteins from various genera in the face
211 microbiome. Surfactin [61,62] is a very powerful surfactant that serves as antibacterial, antiviral,
212 antifungal, and attacks red blood cells with deadly efficiency.
213
214 Biofilm and colonization resistance: The presence of biofilm forming bacteria has been
215 suggested to play a protective role for the host [63]. We identified the biofilm-forming bacteria
216 Pseudomonas fluorescens [64] in higher abundance in the face and as part of the strict taxonomic
217 face microbiome core. Interestingly, in the gut functional core, we identified biofilm formation
218 promoter proteins from F. mortiferum, such as sialic acid-binding periplasmic protein [65], and
219 rubrerythrin [66]. And from C. perfringens, such as UDP-glucuronic acidepimerase [67], putative
220 alginate biosynthesis protein AlgI [68], and fibronectin-binding protein [69], as well as toxin-
221 antitoxin biofilm protein from E. coli [70] (Additional File 8). These results suggest that potentially
222 pathogenic bacteria could form biofilms which allow them to thrive in the gut.
223
224 Pathogenic biofilm formation: Notably, a biofilm-mediated protection scenario requires a special
225 interaction with the vulture’s immune response, otherwise a scenario such as that in the biofilm
226 formation in patients with cystic fibrosis (CF) would develop. The biofilm in CF patients results
227 in clinical symptoms due to the host immune response producing tissue damage as a result of the
10 228 chronic inflammation mediated by the immune complex that is trying to attack the highly resistant
229 bacteria in the biofilm [71]. Thus, the colonization resistance mechanism of the vulture
230 microbiome mediated by the biofilm formation requires that the vulture’s immune system does not
231 react against with a chronic inflammatory response. Interestingly, the
232 PIK3AP1 and TNFAIP3 genes, involved in B-cell development, antigen presentation, auto-
233 inflammation, and NF-kappa B activation, have been found to contain potentially functional
234 altering amino acid changes in the cinereous vulture (Aegypius monachus) [72]. Even more, in CF
235 patients it has been shown that sub-minimal inhibitory concentrations of some antibiotics, such as
236 erythromycin (from which we identified related genes in our nr gene set, Additional File 6) and
237 azithromycin, suppress the production of exoproducts, such as proteases and phospholipase C [73–
238 75]. The inhibition of these exoproducts reduces the antigenic load and thus could lead to the
239 decrease of immune system response. Similar modulatory mechanisms could be taking place in
240 the vulture gut microbiome, were we identified various antibiotics.
241
242 Supplementary Note 6. Resistance genes
243 In the ResFinder database search, we identified resistance genes in 17 out of the 33 face samples
244 (min= 6, 1st Qu= 18, median= 36, mean= 44.35, 3rd Qu= 72, max= 107), and in 36 out of the 46
245 gut samples (min= 6, 1st Qu= 10, median= 15, mean= 19.31, 3rd Qu= 25, max= 59), totalling 215
246 genes (166 in the face, and 139 in the gut) against 15 substances (15 in the face, and 14 in the gut).
247 There is no statistical difference in the number of substances with resistance genes identified by
248 vulture species (P= 0.30, C. atratus mean= 4.175, C. aura mean= 3.405), neither by sample type
249 (P= 0.92, gut mean= 3.84, face mean= 3.76), however there is a difference in the abundance, being
250 more abundant in the gut microbiome (P= 0.018, gut normalized mean= 88,016.84, face
11 251 normalized mean= 56,985.73) (Figure S14). The one substance with resistance genes in the most
252 number of samples (52) is tetracycline, and there is no substance with resistance genes in more
253 than 90% of the samples. In at least 50% of the face and gut samples there are resistance genes for
254 aminoglycoside, lincosamide, macrolides, and tetracycline. Only face samples were found to
255 contain resistance genes against sulphonamide. Interestingly, in the gut dataset there is an
256 abundance of genes resistant to lincosamide, which is used to treat pseudomembranous colitis
257 caused by C. difficile [76].
258 Searching against the Resfams database, we identified 170 different resistance genes in the face,
259 and 170 in the gut, totalling 170 unique resistance proteins. Samples have a minimum of 0
260 resistance proteins (one face sample) and a maximum of 170 (4 gut samples and 2 face samples),
261 with a mean of 104.3 proteins per sample, with each resistance protein being present in a mean
262 number of 47.23 samples (Figure S13C). There is a significant difference in the number of
263 identified proteins with resistance to antibiotics between face and gut (P= 0.049, face mean= 87.3,
264 gut mean= 117.0) (Figure S13A), although there is no statistical difference in the abundance (P=
265 0.69). The protein present in the most number of samples (69) is from the phosphotransferase
266 enzyme family, which confers resistance to various aminoglycosides [77]. The resistance genes
267 identified from the ResFams search can be classified as resistant to the following types of drugs:
268 i) for treatment of various diseases, such as urinary and respiratory diseases, meningitis,
269 tuberculosis, and against Staphylococcus and Streptococcus, ii) for the treatment of enteric
270 diseases, and iii) for the treatment of other diseases caused by fungi or protozoa. Interestingly,
271 there were also genes resistant to indiscriminate antibiotics, such as surfactants, organic solvents,
272 heavy metal ions, antifolates, and carcinogens and anticarcinogens.
273
12 274 Among the most abundant genes from the face MOCAT nr gene set we found antibiotic resistance
275 genes for aminoglycoside from A. baumanii, and kanamycin from Staphylococcus epidermidis. In
276 the search of the face dataset against the ResFinder database we identified a differentially abundant
277 number of resistance genes to macrolide. Given that some macrolides have antibiotic or antifungal
278 activity [78,79], their higher abundance in the face is expected taking into account that the face
279 has a significantly greater fungi diversity (P= 0.029), with many of them being derived from plant
280 pathogens. The face microbiome also contains more resistance genes towards phenicol than the
281 gut microbiome (rescaled mean face= 112,149.94, rescaled mean gut= 2,177.54). Their use against
282 infections in body parts such as eye and ear [80] could explain their higher abundance in the face
283 microbiome. In the ResFams database search we also identified resistance genes to drugs for the
284 treatments of diseases such as enteric diseases (e.g. streptogramin [81] and bicyclomycin [82]),
285 and tuberculosis (e.g. aminoglycoside [83] and oxazolidinones [84]). Interestingly, many of the
286 antibiotics with a resistance gene also pose serious adversities to the vulture, such as macrolides
287 [85] and cephalosporin [86], which cause digestive disturbances to humans.
288
289 References
290 1. Lattanzio V, Lattanzio VMT, Cardinali A. Role of Polyphenols in the Resistance
291 Mechanisms of Plants Against Fungal Pathogens and Insects. In: Phytochemistry:
292 Advances in research. Research Signpost; 2006. p. 23–67.
293 2. Falcone Ferreyra ML, Rius SP, Casati P. Flavonoids: biosynthesis, biological functions,
294 and biotechnological applications. Front Plant Sci. 2012 Jan;3:222.
295 3. Vogt T. Phenylpropanoid biosynthesis. Mol Plant. 2010 Jan;3(1):2–20.
296 4. Dent BB, Forbes SL, Stuart BH. Review of human decomposition processes in soil.
13 297 Environ Geol. 2004 Feb 1;45(4):576–85.
298 5. Evans WED. The chemistry of death. Charles C. Thomas; 1960.
299 6. Mayr D, Margesin R, Klingsbichel E, Hartungen E, Jenewein D, Schinner F, et al. Rapid
300 detection of meat spoilage by measuring volatile organic compounds by using proton
301 transfer reaction mass spectrometry. Appl Environ Microbiol. 2003 Aug;69(8):4697–705.
302 7. Phan N-T, Kim K-H, Jeon E-C, Kim U-H, Sohn JR, Pandey SK. Analysis of volatile
303 organic compounds released during food decaying processes. Environ Monit Assess. 2012
304 Mar;184(3):1683–92.
305 8. Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, et al. Complete genome
306 sequence of Cellulophaga lytica type strain (LIM-21). Stand Genomic Sci. 2011 Apr
307 29;4(2):221–32.
308 9. Bertolini JM, Rohovec JS. Electrophoretic detection of proteases from different
309 Flexibacter columnaris strains and assessment of their variability. Dis Aquat Organ.
310 1992;12:121–8.
311 10. Declercq AM, Haesebrouck F, Van den Broeck W, Bossier P, Decostere A. Columnaris
312 disease in fish: a review with emphasis on bacterium-host interactions. Vet Res. BioMed
313 Central; 2013 Jan 24;44(1):27.
314 11. Ramezani M, MacIntosh SE, White RL. Utilization of D-amino acids by Fusobacterium
315 nucleatum and Fusobacterium varium. Amino Acids. 1999 Jan;17(2):185–93.
316 12. Wahren A, Holme T. Amino acid and peptide requirement of Fusiformis necrophorus. J
317 Bacteriol. 1973 Oct;116(1):279–84.
318 13. Budd A, Blandin S, Levashina EA, Gibson TJ. Bacterial alpha2-macroglobulins:
319 colonization factors acquired by horizontal gene transfer from the metazoan genome?
14 320 Genome Biol. 2004 Jan;5(6):R38.
321 14. Cáceres LC, Bonacci GR, Sánchez MC, Chiabrando GA. Activated α(2) macroglobulin
322 induces matrix metalloproteinase 9 expression by low-density lipoprotein receptor-related
323 protein 1 through MAPK-ERK1/2 and NF-κB activation in macrophage-derived cell lines.
324 J Cell Biochem. 2010 Oct 15;111(3):607–17.
325 15. Lin AH-M, Nichols BL, Quezada-Calvillo R, Avery SE, Sim L, Rose DR, et al.
326 Unexpected high digestion rate of cooked starch by the Ct-maltase-glucoamylase small
327 intestine mucosal α-glucosidase subunit. PLoS One. 2012 Jan;7(5):e35473.
328 16. Slaughter SL, Ellis PR, Butterworth PJ. An investigation of the action of porcine
329 pancreatic alpha-amylase on native and gelatinised starches. Biochim Biophys Acta. 2001
330 Feb 16;1525(1–2):29–36.
331 17. Wong SG, Dessen A. Structure of a bacterial α2-macroglobulin reveals mimicry of
332 eukaryotic innate immunity. Nat Commun. Nature Publishing Group; 2014 Jan 15;5:4917.
333 18. Stevens DL, Bryant AE. The Role of Clostridial Toxins in the Pathogenesis of Gas
334 Gangrene. Clin Infect Dis. Oxford University Press; 2002 Sep 1;35(s1):S93–100.
335 19. Brooke JS. Stenotrophomonas maltophilia: an emerging global opportunistic pathogen.
336 Clin Microbiol Rev. 2012 Jan;25(1):2–41.
337 20. Roggenbuck M, Bærholm Schnell I, Blom N, Bælum J, Bertelsen MF, Pontén TS, et al.
338 The microbiome of New World vultures. Nat Commun. Nature Publishing Group; 2014
339 Nov 25;5:5498.
340 21. Garnier T, Cole ST. Complete nucleotide sequence and genetic organization of the
341 bacteriocinogenic plasmid, pIP404, from Clostridium perfringens. Plasmid. 1988
342 Mar;19(2):134–50.
15 343 22. El-Sayed AK, Hothersall J, Cooper SM, Stephens E, Simpson TJ, Thomas CM.
344 Characterization of the mupirocin biosynthesis gene cluster from Pseudomonas
345 fluorescens NCIMB 10586. Chem Biol. 2003 May;10(5):419–30.
346 23. Kallimanis A, Frillingos S, Drainas C, Koukkou AI. Taxonomic identification,
347 phenanthrene uptake activity, and membrane lipid alterations of the PAH degrading
348 Arthrobacter sp. strain Sphe3. Appl Microbiol Biotechnol. 2007 Sep;76(3):709–17.
349 24. Pawlowski DR, Raslawsky A, Siebert G, J Metzger D. Identification of Hylemonella
350 gracilis as an Antagonist of Yersinia pestis Persistence. J Bioterror Biodef. OMICS
351 International; 2011 Feb 10;2(S3).
352 25. Murakami K, Habukawa C, Nobuta Y, Moriguchi N, Takemura T. The effect of
353 Lactobacillus brevis KB290 against irritable bowel syndrome: a placebo-controlled
354 double-blind crossover trial. Biopsychosoc Med. BioMed Central; 2012 Jan 3;6(1):16.
355 26. Hochwind K, Weinmaier T, Schmid M, van Hemert S, Hartmann A, Rattei T, et al. Draft
356 genome sequence of Lactobacillus casei W56. J Bacteriol. 2012 Dec 1;194(23):6638.
357 27. Bendali F, Madi N, Sadoun D. Beneficial effects of a strain of Lactobacillus paracasei
358 subsp. paracasei in Staphylococcus aureus-induced intestinal and colonic injury. Int J
359 Infect Dis. 2011 Nov;15(11):e787-94.
360 28. Martín R, Jiménez E, Olivares M, Marín ML, Fernández L, Xaus J, et al. Lactobacillus
361 salivarius CECT 5713, a potential probiotic strain isolated from infant feces and breast
362 milk of a mother-child pair. Int J Food Microbiol. 2006 Oct 15;112(1):35–43.
363 29. Cadieux P, Wind A, Sommer P, Schaefer L, Crowley K, Britton RA, et al. Evaluation of
364 reuterin production in urogenital probiotic Lactobacillus reuteri RC-14. Appl Environ
365 Microbiol. 2008 Aug;74(15):4645–9.
16 366 30. Casas IA, Dobrogosz WJ. Validation of the Probiotic Concept: Lactobacillus reuteri
367 Confers Broad-spectrum Protection against Disease in Humans and Animals. Microb Ecol
368 Heal Dis. 2000 Dec 1;12(4).
369 31. Williams JD, Jacobson EL, Kim H, Kim M, Jacobson MK. Folate in skin cancer
370 prevention. Subcell Biochem. 2012 Jan;56:181–97.
371 32. Brünke P, Sterner O, Bailey JE, Minas W. Heterologous expression of the
372 naphthocyclinone hydroxylase gene from Streptomyces arenae for production of novel
373 hybrid polyketides. Antonie Van Leeuwenhoek. 2001 Sep;79(3–4):235–45.
374 33. Straub D, Rothballer M, Hartmann A, Ludewig U. The genome of the endophytic
375 bacterium H. frisingense GSF30(T) identifies diverse strategies in the Herbaspirillum
376 genus to interact with plants. Front Microbiol. Frontiers; 2013 Jan 27;4:168.
377 34. Rashel M, Uchiyama J, Ujihara T, Uehara Y, Kuramoto S, Sugihara S, et al. Efficient
378 elimination of multidrug-resistant Staphylococcus aureus by cloned lysin derived from
379 bacteriophage phi MR11. J Infect Dis. 2007 Oct 15;196(8):1237–47.
380 35. Mumm IP, Wood TL, Chamakura KR, Kuty Everett GF. Complete Genome of
381 Acinetobacter baumannii Podophage Petty. Genome Announc. 2013 Jan;1(6).
382 36. Merabishvili M, Vandenheuvel D, Kropinski AM, Mast J, De Vos D, Verbeken G, et al.
383 Characterization of newly isolated lytic bacteriophages active against Acinetobacter
384 baumannii. PLoS One. 2014 Jan;9(8):e104853.
385 37. Liu M, Deora R, Doulatov SR, Gingery M, Eiserling FA, Preston A, et al. Reverse
386 transcriptase-mediated tropism switching in Bordetella bacteriophage. Science. American
387 Association for the Advancement of Science; 2002 Mar 15;295(5562):2091–4.
388 38. Kwoh DY, Kemper J. Bacteriophage P22-mediated specialized transduction in Salmonella
17 389 typhimurium: high frequency of aberrant prophage excision. J Virol. 1978 Sep;27(3):519–
390 34.
391 39. Garcia E, Chain P, Elliott JM, Bobrov AG, Motin VL, Kirillina O, et al. Molecular
392 characterization of L-413C, a P2-related plague diagnostic bacteriophage. Virology. 2008
393 Mar 1;372(1):85–96.
394 40. Govind R, Vediyappan G, Rolfe RD, Dupuy B, Fralick JA. Bacteriophage-mediated toxin
395 gene regulation in Clostridium difficile. J Virol. 2009 Dec;83(23):12037–45.
396 41. Barbirz S, Müller JJ, Uetrecht C, Clark AJ, Heinemann U, Seckler R. Crystal structure of
397 Escherichia coli phage HK620 tailspike: podoviral tailspike endoglycosidase modules are
398 evolutionarily related. Mol Microbiol. 2008 Jul;69(2):303–16.
399 42. Horgan M, O’Sullivan O, Coffey A, Fitzgerald GF, van Sinderen D, McAuliffe O, et al.
400 Genome analysis of the Clostridium difficile phage PhiCD6356, a temperate phage of the
401 Siphoviridae family. Gene. 2010 Aug 15;462(1–2):34–43.
402 43. Kagawa H, Ono N, Enomoto M, Komeda Y. Bacteriophage chi sensitivity and motility of
403 Escherichia coli K-12 and Salmonella typhimurium Fla- mutants possessing the hook
404 structure. J Bacteriol. 1984 Feb;157(2):649–54.
405 44. Berry C. The bacterium, Lysinibacillus sphaericus, as an insect pathogen. J Invertebr
406 Pathol. 2012 Jan;109(1):1–10.
407 45. Vodovar N, Vallenet D, Cruveiller S, Rouy Z, Barbe V, Acosta C, et al. Complete genome
408 sequence of the entomopathogenic and metabolically versatile soil bacterium
409 Pseudomonas entomophila. Nat Biotechnol. 2006 Jun;24(6):673–9.
410 46. Vodovar N, Vinals M, Liehl P, Basset A, Degrouard J, Spellman P, et al. Drosophila host
411 defense after oral infection by an entomopathogenic Pseudomonas species. Proc Natl
18 412 Acad Sci U S A. 2005 Aug 9;102(32):11414–9.
413 47. Höltzel A, Kempter C, Metzger JW, Jung G, Groth I, Fritz T, et al. Spirofungin, a new
414 antifungal antibiotic from Streptomyces violaceusniger Tü 4113. J Antibiot (Tokyo). 1998
415 Aug;51(8):699–707.
416 48. Kang MJ, Strap JL, Crawford DL. Isolation and characterization of potent antifungal
417 strains of the Streptomyces violaceusniger clade active against Candida albicans. J Ind
418 Microbiol Biotechnol. 2010 Jan;37(1):35–41.
419 49. Ichikawa N, Oguchi A, Ikeda H, Ishikawa J, Kitani S, Watanabe Y, et al. Genome
420 sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family
421 Streptomycetaceae. DNA Res. 2010 Dec;17(6):393–406.
422 50. Wang X-J, Yan Y-J, Zhang B, An J, Wang J-J, Tian J, et al. Genome sequence of the
423 milbemycin-producing bacterium Streptomyces bingchenggensis. J Bacteriol. 2010 Sep
424 1;192(17):4526–7.
425 51. Chattopadhyay A, Bhatnagar NB, Bhatnagar R. Bacterial insecticidal toxins. Crit Rev
426 Microbiol. 2004 Jan;30(1):33–54.
427 52. Landolt C. Dictyostelid Cellular Slime Molds from Caves. J Cave Karst Stud.
428 2006;68(1):22–6.
429 53. Flot J-F, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EGJ, et al. Genomic evidence
430 for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. Nature Publishing
431 Group, a division of Macmillan Publishers Limited. All Rights Reserved.; 2013 Aug
432 22;500(7463):453–7.
433 54. Hoshino T. Violacein and related tryptophan metabolites produced by Chromobacterium
434 violaceum: biosynthetic mechanism and pathway for construction of violacein core. Appl
19 435 Microbiol Biotechnol. 2011 Sep;91(6):1463–75.
436 55. Hornung C, Poehlein A, Haack FS, Schmidt M, Dierking K, Pohlen A, et al. The
437 Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and
438 L. pneumophila LqsA autoinducer synthases. PLoS One. Public Library of Science; 2013
439 Jan 6;8(2):e55045.
440 56. Jeon CO, Park W, Ghiorse WC, Madsen EL. Polaromonas naphthalenivorans sp. nov., a
441 naphthalene-degrading bacterium from naphthalene-contaminated sediment. Int J Syst
442 Evol Microbiol. 2004 Jan;54(Pt 1):93–7.
443 57. Vass AA, Smith RR, Thompson C V, Burnett MN, Wolf DA, Synstelien JA, et al.
444 Decompositional odor analysis database. J Forensic Sci. 2004 Jul;49(4):760–9.
445 58. Forbes SL, Perrault KA. Decomposition odour profiling in the air and soil surrounding
446 vertebrate carrion. PLoS One. Public Library of Science; 2014 Jan 16;9(4):e95107.
447 59. Fontes GC, Ramos NM, Amaral PFF, Nele M, Coelho MAZ. Renewable resources for
448 biosurfactant production by yarrowia lipolytica. Brazilian J Chem Eng. Associação
449 Brasileira de Engenharia Química; 2012 Sep;29(3):483–94.
450 60. Pacheco GJ, Ciapina EMP, Gomes E de B, Junior NP. Biosurfactant production by
451 rhodococcus erythropolis and its application to oil removal. Braz J Microbiol. 2010
452 Jul;41(3):685–93.
453 61. Das P, Mukherjee S, Sen R. Genetic regulations of the biosynthesis of microbial
454 surfactants: an overview. Biotechnol Genet Eng Rev. 2008 Jan;25:165–85.
455 62. Mor A. Peptide-based antibiotics: A potential answer to raging antimicrobial resistance.
456 Drug Dev Res. 2000 Jul;50(3–4):440–7.
457 63. Mertz PM, Eaglstein WH. The effect of a semiocclusive dressing on the microbial
20 458 population in superficial wounds. Arch Surg. 1984 Mar;119(3):287–9.
459 64. O’Toole GA, Kolter R. Initiation of biofilm formation in Pseudomonas fluorescens
460 WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. Mol
461 Microbiol. 1998 May;28(3):449–61.
462 65. Swords WE, Moore ML, Godzicki L, Bukofzer G, Mitten MJ, VonCannon J. Sialylation
463 of lipooligosaccharides promotes biofilm formation by nontypeable Haemophilus
464 influenzae. Infect Immun. 2004 Jan;72(1):106–13.
465 66. Jiao Y, D’haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, et al.
466 Identification of biofilm matrix-associated proteins from an acid mine drainage microbial
467 community. Appl Environ Microbiol. 2011 Aug;77(15):5230–7.
468 67. Schmid J, Sieber V, Rehm B. Bacterial exopolysaccharides: biosynthesis pathways and
469 engineering strategies. Front Microbiol. Frontiers; 2015 Jan 26;6:496.
470 68. Rehm BH, Valla S. Bacterial alginates: biosynthesis and applications. Appl Microbiol
471 Biotechnol. 1997 Sep;48(3):281–8.
472 69. McCourt J, O’Halloran DP, McCarthy H, O’Gara JP, Geoghegan JA. Fibronectin-binding
473 proteins are required for biofilm formation by community-associated methicillin-resistant
474 Staphylococcus aureus strain LAC. FEMS Microbiol Lett. 2014 Apr;353(2):157–64.
475 70. Kim Y, Wang X, Ma Q, Zhang X-S, Wood TK. Toxin-antitoxin systems in Escherichia
476 coli influence biofilm formation through YjgK (TabA) and fimbriae. J Bacteriol. 2009 Feb
477 15;191(4):1258–67.
478 71. Høiby N, Krogh Johansen H, Moser C, Song Z, Ciofu O, Kharazmi A. Pseudomonas
479 aeruginosa and the in vitro and in vivo biofilm mode of growth. Microbes Infect. 2001
480 Jan;3(1):23–35.
21 481 72. Chung O, Jin S, Cho YS, Lim J, Kim H, Jho S, et al. The first whole genome and
482 transcriptome of the cinereous vulture reveals adaptation in the gastric and immune
483 defense systems and possible convergent evolution between the Old and New World
484 vultures. Genome Biol. 2015 Oct 21;16(1):215.
485 73. Sakata K, Yajima H, Tanaka K, Sakamoto Y, Yamamoto K, Yoshida A, et al.
486 Erythromycin inhibits the production of elastase by Pseudomonas aeruginosa without
487 affecting its proliferation in vitro. Am Rev Respir Dis. 1993 Oct;148(4 Pt 1):1061–5.
488 74. Molinari G, Guzmán CA, Pesce A, Schito GC. Inhibition of Pseudomonas aeruginosa
489 virulence factors by subinhibitory concentrations of azithromycin and other macrolide
490 antibiotics. J Antimicrob Chemother. 1993 May;31(5):681–8.
491 75. Kobayashi H. Airway Biofilm Disease: Clinical Manifestations and Therapeutic
492 Possibilities Using Macrolides. J Infect Chemother. Springer-Verlag; 1995;1(1):1–15.
493 76. Mullany P, Wilks M, Tabaqchali S. Transfer of macrolide-lincosamide-streptogramin B
494 (MLS) resistance in Clostridium difficile is linked to a gene homologous with toxin A and
495 is mediated by a conjugative transposon, Tn5398. J Antimicrob Chemother. 1995
496 Feb;35(2):305–15.
497 77. Sarwar M, Akhtar M. Cloning of aminoglycoside phosphotransferase (APH) gene from
498 antibiotic-producing strain of Bacillus circulans into a high-expression vector, pKK223-3.
499 Purification, properties and location of the enzyme. Biochem J. 1990 Jun 15;268(3):671–
500 7.
501 78. Aszalos A, Bax A, Burlinson N, Roller P, McNeal C. Physico-chemical and
502 microbiological comparison of nystatin, amphotericin A and amphotericin B, and structure
503 of amphotericin A. J Antibiot (Tokyo). 1985 Dec;38(12):1699–713.
22 504 79. Zotchev SB. Polyene macrolide antibiotics and their applications in human therapy. Curr
505 Med Chem. 2003 Feb;10(3):211–23.
506 80. Bron AJ, Leber G, Rizk SN, Baig H, Elkington AR, Kirkby GR, et al. Ofloxacin
507 compared with chloramphenicol in the management of external ocular infection. Br J
508 Ophthalmol. 1991 Nov;75(11):675–9.
509 81. Johnston NJ, Mukhtar TA, Wright GD. Streptogramin antibiotics: mode of action and
510 resistance. Curr Drug Targets. 2002 Aug;3(4):335–44.
511 82. Kohn H, Widger W. The molecular basis for the mode of action of bicyclomycin. Curr
512 Drug Targets Infect Disord. 2005 Sep;5(3):273–95.
513 83. Investigation MRC. Streptomycin treatment of pulmonary tuberculosis. Br Med J. 1948
514 Oct 30;2(4582):769–82.
515 84. Cynamon MH, Klemens SP, Sharpe CA, Chase S. Activities of Several Novel
516 Oxazolidinones against Mycobacterium tuberculosis in a Murine Model. Antimicrob
517 Agents Chemother. 1999 May 1;43(5):1189–91.
518 85. Periti P, Mazzei T, Mini E, Novelli A. Adverse effects of macrolide antibacterials. Drug
519 Saf. 1993 Nov;9(5):346–64.
520 86. Norrby SR. Side effects of cephalosporins. Drugs. 1987 Jan;34 Suppl 2:105–20.
521
522
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