Microbes are more dynamic and inducible to yield new compounds than plants- as per bookish knowledge that I have !

Secondary metabolites are more favored to obtain from plants than other sources since plants are easily available and store secondary metabolites in major organs (Roots, leaves, fruits etc.). Conversely microbes secrete their secondary metabolites in the environment while animals often produce secondary metabolites only on demand or store them in localized or specialized organs.

For further detail and reference you may consult to "Natural Product Chemistry for Drug Discovery" 2010. edited by Antony D. Buss, Mark S. Butler

In my experience, microbial secondary natural products are tremendously diverse using a range of biosynthetic machineries that include NRPS, PKS, hybrids, terpene, as well as glycosyl trasnferases. Plants often contain alkaloid, flavanoid, terpene, and carbohydrate biosynthetic operons (among others) and, although they produce a lot of the compounds, they are usually analogues of a known scaffold. I speculate that plants have long been the major source for natural products due to the ease of purification and growth, but this does not speak to the metabolic diversity. 

If you are looking for novel scaffolds you have a better chance looking with microbial species as opposed to plants. In particular, fungi are incredibly diverse with tremendous biosynthetic potential.  The actinobacteria have high biosynthetic potential, but their yield is very low (often requiring 40-80 L for a large scale fermentation). The Pseudomonads have high biosynthetic potential, but have been well studied.

Finally, co-culturing is an interesting technique as well... Co-cultures with multiple fungi types, bacterial with multiple types, and mixtures between both fungi and bacteria have yielded interesting natural products that were otherwise undetected.

In the end, your best bet is to isolate secondary metabolites from unstudied species of fungi or bacteria. If you HAVE to stay with plants then hunt for uncharacterized species with little homology as everything else has already been studied!

Thank you all guy's for your feed backs...

I think from your answers it seems that it's a debatable topic. ..Dr Carter, I do agree withall 

I think Microbes are the best source for novel chemicals, as mentioned by Dr Carter most of them are uncharacterized. We cannot forget the serendipity of Penicillin discovery. On the contrary plants have been good source of secondary metabolites too but their potentials are over weighed by microbes.

Both plants and microbes serve as a good source of secondary metabolites but herbal plants have got plenty  and potential natural compounds as secondary metabolites.

Highly agreed with Huma Qureshi, Manisha Mohapatra and Vaidya Vasant Patil.

https://www.researchgate.net/publication/268389305_NISHAN-E-ZAFAR

Regards

Microbes are better than plants for producing secondary metabolites.

Plant endopyhtes : new trend

Plant kingdom is widely distributed. Easily available. Enriched with various types of secondary metabolites. 

Microbes even good source of secondary metabolites. If you see the discovered drug source from these two groups, they are equally studied and introduced to the market. Antibiotics in general obtained from microbes. They are equally favoured. 

But plants are favoured more because of its wide distribution and natural way of available secondary metabolites when compared to other sources.