Purely from a microbiome study perspective there were many big publications this year... but I'll put a few
I think that CRIPSR has had a huge year, breaking into the clinical space and actually being used successfully to treat adult patients. I think WGS metagenomics is having a big year too and soon we may be leaving amplicon based methods in the past (despite being cheaper and arguably better, at least for bacteria). The future is in WGS methods. We also seem to be establishing better and more consistent methodologies for analyzing microbiome data, whereas last year it seemed that every lab was doing things their own way (still, of course, its like that - but less so).
Anyway, for the microbiome stuff, we are finding stronger links between signatures in our gut microbiome to diseases (neurological and gut) but also in the metabolism and effects of pharmaceutical medicines. We also are finding links in the development of neurological disorders like Autism among numerous other diseases (obesity, diabetes, etc). Here are a few that were published in Nature this year that I think will have an impact on how we think about our microbiome and its interactions with disease/medicine/our immune system:
(1) Dynamics of the human gut microbiome in inflammatory bowel disease - https://www.nature.com/articles/nmicrobiol20174
(2) Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome - http://onlinelibrary.wiley.com/doi/10.1002/mds.26942/abstract
(3) Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug - https://www.nature.com/articles/nm.4345
(4) Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patient - http://www.neoplasia.com/article/S1476-5586%2817%2930238-5/fulltext
(5) A communal catalogue reveals Earth’s multiscale microbial diversity - https://www.nature.com/articles/nature24621
There are too many papers for me to sift through right now and make a choice, but I put some I found interesting/were in high impact journals (namely, Nature).