saddybenzene

If you aren't getting along with your PI to that degree, I suggest finding a new lab. That environment won't be conducive to your success anyway.
You should have your current PI as a letter writer when you apply, which is why I suggest finding a new letter writer asap.
Alternatively to your PI, if you work directly with a postdoc and have a good relationship with them, they can write your letter.
It matters less who wrote the letter than that it's a great letter. 

Hi!
I am currently a post-bac at NIH, as far as, the GW-NIH program goes; I thought about applying to that however, they are currently looking for a new program admin of the program (who would make sure you're meeting your milestones) so I was advised against it if they dont have a strong one. As of right now, I dont think they do. Second, they typically dont accept people out-side of the nih post-bac program. This is because NIH PI's are different than ones in academia. NIH PIs don't go for low-hanging fruit which isn't what you may need when you are trying to finish your thesis.  

Congrats! May I ask which program?

Hey! I'm applying this year for Microbiology as well, and I stumbled across the Biomed faculty at The University of Chicago which has a major focus on the microbiome and immunology, in particular Dr. Alexander Chervonsky who you might want to check out!

Hey your application profile looks great! I'd recommend also looking at UCSF. I think you'd be a competitive applicant there and they have a lot of great immunology and microbiome research. Susan Lynch in particular is doing some really cool microbiome stuff. Plus SF has a wonderful temperate climate!

You should look up Dr. Andy Kau's research at WUSTL. I work in the lab next to his and they are doing some pretty neat immuno/micro stuff with the gut microbiome 

I'm rotation right now through the Microbiology & Immunology (combined) department at UMich. If you're looking for an umbrella program, they have PIBS, which allows you to rotate in 14 different departments to find your fit. It is also walkable/bikeable and not too hot.
You can see current student statistics here (choose Microbiology & Immunology in the top Field of Study drop down menu): https://tableau.dsc.umich.edu/t/UM-Public/views/RackhamDoctoralProgramStatistics/ProgramStatistics?:embed=y&:showAppBanner=false&:showShareOptions=true&:display_count=no&:showVizHome=no&FOSDParameter=All+Rackham

If you're looking at UVA, John Luken's lab might be kinda up your alley. He's in the Center for Brain Immunology and Glia which is in the Neuroscience Department, but most of the professors in that center are actually immunologists for the most part.

Hey, from your numerical stats you look like an excellent candidate and I'd say you'd have a good shot at the schools you listed. What it really comes down to now is if your recommendation letter writers will be able to step up and vouch for your ability and character. Also, it will be super important that you're able to articulate the big picture and significance of the research you did both in your statements and during interviews.
If teaching is important to you, you may want to consider non-medical center based biology programs. Typically, at medical schools, teaching is usually optional and your stipend is guaranteed through your research. At traditional universities with an undergraduate base, teaching is usually a required part of your compensation package. From my experience of interviewing at phd programs based in medical schools, there are less opportunities to TA, just by the lack of undergraduates to teach. Not saying that there are absolutely no TA opportunities, there are just less of them. I think Berkeley and Princeton would be great schools to apply to with your interests. I know Houston is very south and a little warm but Baylor College of Medicine has a stellar microbiome center with research faculty that closely align with your interests. Other schools with strong microbiology departments you might want to consider are: Harvard, UNC, University of Washington, Emory, UMich, Yale.

Hi there,
I'm also in the Boston area. There are plenty of academic labs here that accept undergraduate volunteers, and as a candidate with a degree already in hand, I'm sure you would be very desirable. I am unfamiliar with oceanography departments around here, but try looking at the websites of Tufts, Harvard, MIT, Suffolk (pretty small department, probably does not encompass your research interests), UMass Boston, Northeastern, BU, Brandeis, and Boston College to name a few. Just look on the biology department faculty pages.
In contacting professors that suit your particular interests, I would suggest attaching a CV and resume. Write a bit about yourself, your research interests, future goals, and why their lab sticks out to you. Try to be concise, and ask them if they would like to speak with you further as a potential volunteer. You will probably have to email a few at a time, because I remember applying to biochemistry labs as a wee undergrad and only getting 3/7 responses (in which only 2 said they were willing to accept new students). If you don't get any responses, feel free to politely prod them again in a week or so, because it's easy for the first message to accidentally slip through the cracks.

Hey there @DaddyBenzene, just here to offer my $0.02 - I would agree with everything biotechie said, and especially reiterate that depending on what field you're in, the ivy league may not actually be the best. For example, in my applications process, a number of public research universities like UC's, University of Washington, UNC Chapel Hill, etc. are much better for the type of research I'm interested in than a lot of the ivy league. Definitely consider program and research fit over name brand or perceived prestige. 
Secondly, I applied this year as a senior in undergrad, and while I'd say it's definitely doable, it is not the norm. At all the interview visits I went to, I'd estimate a solid 90% of the interviewees had taken at least one "gap year" between undergrad and grad school to gain experience or just to make sure that a Ph.D. was the route they wanted to take. However, just speaking from my personal experience, as long as you curate your application list well (i.e. do your homework and make sure the places you're applying to are places you really really want to go to and where you see your interests matching really well with ideally at least 3 faculty members per program), I think there's no harm in applying. Even if the worst happens, you can always take a year to boost your CV and reapply the next year. 

Seconding eevee - I got in direct from undergrad with no publications or conference presentations so it's definitely possible. And at my interviews I'd say somewhere between 1/4 and 1/2 of applicants were direct from undergrad depending on the school and a lot of current grad students said their cohort was about half and half direct vs gap year(s). 

You're welcome!

The stats you see here represent a very small proportion of the applicant field, and honestly, after seeing the stats here, many people choose not to share theirs because they think they don't "measure up." Based on what you've said here, unless you have some weird black mark on your record, you should definitely be able to get into a graduate program somewhere. If you limit yourself to schools that have strict cutoffs for GRE and GPA, you might have less luck, but I think that sort of system is a poor measure of a scientist because the GRE and GPA only measure your ability to take tests, not be a scientist. That's a big reason I regretted one of my applications as I found out later that they were using that cutoff. Programs I applied to that don't:
Baylor College of Medicine (Interdisciplinary, but they are restructuring the grad programs starting 2019 admits)
University of Florida (Interdisciplinary)
University of Utah (Good epigenetics)
University of California at San Diego (Lots of good stuff)

Feel free to DM me if you have specific questions you don't want to ask here.

Hey there! I got the opportunity to help with recruitment a couple of years ago; we didn't really look for publications. Instead we looked to see that people had worked in labs. Often people have papers as a consequence of experience, but I'd say only about 1/4 of applicants actually had them. I didn't, and my papers from the M.S. STILL aren't published. What seems to be most important is that you understand the research process and that your letters reflect this as much as the dates on your CV. 16 months of solid lab experience looks better to the AdComm than a summer REU at a prestigious university because that means you were in a lab long enough to really learn science. The fact that you will have a M.S. (assuming it is a research-based, science masters) also gives you a leg up.
Long story short: Don't worry about papers. Don't defer your application. Just make sure you're a good scientist.
Finally, and most importantly, don't view Ivy's as the "best" schools; you may feel happier and more at home at one of the ones you're calling a safety, and you should go where you feel best. If you're interested in a niche field, there are large amounts of people studying things you're interested in at a smaller school, such as UTSW for me in the lipid field. Choose your schools for the program and the PIs (early to mid-career are best) that you want to work under and then aim for Ivy's or big-name PIs for your postdoc when you need less guidance. I'm telling you this from my own positive experience with a brand new PI and from watching my peers struggle in big labs where they get little attention from their mentor. I'm about to graduate with multiple first-author papers and several co-authors, so I'm set up well to get a good postdoc (or industry job).

From what I've heard, publications are not the end all be all when it comes to graduate admissions.  Have you at least presented your research at a conference in a poster or oral format?  If you feel you are ready to apply next Fall (and it sounds like you have a bit of research experience under your belt), I think you have a shot.  I have a couple first author pubs in preparation right now, and I just mentioned it in my personal statement, and during my interviews, my interviewers seemed impressed when I talked about it.  So even if the paper isn't actually published, you can still mention it as in preparation, in submission, in review, etc.
For lit reviews, I haven't done one of those, so I'm not sure what that all entails.  But I imagine getting anything published in a reputable journal would be difficult without a PI backing you up.