Silver is best. 

Because of the high oxidation potential, aggregation, and toxicity of silver NPs, gold should be use. Also, gold is inert and highly stable in buffered solution. 

gold and silver is widely used in SERS for detection of biomolecules

Its Au and Ag Nps. Au Nps are more preferred due to compatibility reasons.

Silver may induce more toxic than gold, silver is suitable for topical applications not safer for in-vivo and gold is compatible when compare with silver.

Au

Dear Priyanka,

I guess you are not really concerned in toxicity of nanoparticles as previous answers suggest. In my experience, gold NP are better, because of different spectral response of the cell wall components. Could you describe in detail what you are expecting from SERS spectra?

Please consider also the excitation wavelength: bacteria have different spectra when excited by different lasers, see also these papers:

Zeiri Efrima (2005) DOI: 10.1002/jrs.1349

Kerr et al (2015) DOI: 10.1039/c5ay00327j

Smith-Palmer et al (2010) doi:10.1016/j.vibspec.2010.02.012

Dear Priyanka,

     There is no "big scientific difference between gold and silver nanoparticles as far as it coating is concerned on the bacterial surface".

     However, a few words of caution, if you please...

     The main trouble is that, before askin what metal is better, one should answer the questions: (1) What component(s) of the bacteria is selectively enhanced and is represented by the SERS spectrum we've observed? and (2) Can we selectively control the part of a bacterium that we would like to observe with the aid of SERS?

      That is because (a) SERS (even of the same type of bacterium) is strongly sensitive to the method of preparation of the SERS-active nanoparticles;(b) The way SERS NPs are brought into contact with the bacteria has a strong effect on the spectra one actually measures; (c) At other excitation wavelengths the spectra can exhibit different SERS bands.

     It's well known that, depending on the SERS colloids preparation mode (e.g. mixing preformed colloids with the bacteria/ vs applying the bacterial sample onto solid SERS support/ vs producing the colloid in the presence of the bacteria) the observed SERS spectra will differ enormously. Depending on the above modes, the SERS activity may be localized on interior of the bacterium (on the cell wall, i.e., be "external") or can be forced into the inner side of the cell wall membrane. Owing to this, SERS spectra can represent the bacterial surface (judging by your question, it's your case - then peptides mainly) or the inner constituents of the bacteria (phospholipids, peptides, coenzymes, sugars, etc.). Thus, independently of gold or silver nanoparticles used, if the answers to above question (1) and (2) are negative, then one should be prepared to manage (interpret) possible irreproducibility and huge difference in measured bacterial SERS spectra observed even for the same bacteria. Please, pay an attention to the above points when planning your SERS experiments with bacteria.

Good Luck!

Alexander Shchegolikhin Thank you for your reply, i am restarting the SERS experiment now and its really helpful to consider all this factors