The over use of antibiotics has been building for years as THE reason why ANTIBIOTIC RESISTANCE has increased. I have been reading additional research on this topic and we should include VACCINES, TOXIC METALS and PESTICIDES to the list.  There are more culprits than just antibiotics that can alter the "beneficial bacteria" of the gut.  To ONLY focus on antibiotics may prove dangerous as alternative antimicrobial approaches could be another tampering by MAN that will be -----  regrettable.   

Let's focus on VACCINES because there seems to be red flags:

It is a common practice for decades to use of sub-therapeutic dose of antibiotics in food-animal feeds to prevent animals from diseases and to improve production performance in modern animal husbandry. In the meantime, concerns over the increasing emergence of antibiotic-resistant bacteria due to the unreasonable use of antibiotics and an appearance of less novelty antibiotics have prompted efforts to develop so-called alternatives to antibiotics. Whether or not the alternatives could really replace antibiotics remains a controversial issue. 

To overcome the increased rate of mortality and morbidity due to the ban of in-feed antibiotics, a number of alternatives/replacements have been proposed. They are antibacterial vaccines, immunomodulatory agents, bacteriophages and their lysins, antimicrobial peptides (AMPs), pro-, pre-, and synbiotics, plant extracts, inhibitors for bacterial quorum sensing (QS), biofilm and virulence, and feed enzymes, etc.. Are these antibiotic alternatives really as effective as antibiotics to control the diseases in animals? ...... Immunity modulating agents (immunomodulators) are used for immunotherapy, which is defined as treatment of disease by inducing, enhancing, or suppressing an immune response. Vaccine is one of the most important immunomodulators, and some pharmaceutical agents could also be used as immunomodulators.

...Traditional vaccines are generally classified into live-attenuated and inactivated/killed vaccines.... However, the major drawbacks of the live strains is that they persist in the animal body for a longer time and have a high risk of reverting to full virulence....Killed vaccines are safer than the live vaccines. It is made by killing in vitro-grown bacterial cultures and packing with oil-based adjuvants to enhance immune responses. They are quite inexpensive in production and stable in storage....However, killed vaccines have numerous disadvantages such as the lack of relevant protective antigens (PAs) due to in vitro growth conditions and killing processes, antigenic competition between non-protective and protective components, a lack of safety due to potentially harmful components such as lipopolysaccharide, and a lack of broad-spectrum protection. In addition, killed vaccines require the use of adjuvants which limits the delivery options for the vaccines. Moreover, most of the killed vaccines are injectable products and are not routinely used in intensive broiler operations.

With the increasing use of bacterins, there are concerns that this may lead to the increasing virulence of bacteria. As an alternative, subunit vaccine is composed of either a single antigen or multiple defined antigens (predominantly proteins). This kind of vaccines lack the regulatory and biological complications associated with the living organisms. On the other hand, subunit vaccines are usually poorly immunogenic, requiring formulation with appropriate adjuvant(s) ...

,,,DNA vaccines offer another promising improvement to conventional vaccines. DNA vaccine is made up of a small, circular piece of bacterial DNA (called a plasmid) that has been genetically engineered to include the DNA sequence(s) encoding the antigen(s) from a pathogen. When the vaccine DNA is injected into the cells of the body, the host cells “reads” the DNA and converts it into pathogenic proteins which would trigger a range of immune responses. Nevertheless, DNA vaccine is limited in its protective capacity to the encoded proteins on the vector and may pose a riskof integrating the genetic elements of the vector into the host genome....Although vaccines against E. coli and Brachyspira hyodysenteriae for treating swine dysentery have been reported, safety and efficacy data are still lacking, hindering the commercialization process of these biological products...

None of that sounds too convincing or safe.  Here then is an interesting addition to this true tale of MICROBIOME concerns for HUMANKIND:

Why Big Pharma Wants to Switch Billions of Farm Animals to Vaccines From Antibiotics 

A sparkling and sprawling 48,000-square-foot two-story structure, decorated with artwork of animals etched onto interior glass walls, recently opened its doors 23 miles outside Indianapolis with one sole purpose: to keep the globe’s 70 billion farm animals healthy...built and operated by Elanco LLC, a unit Eli Lilly & Co., is focused exclusively on developing vaccines as alternatives. It’s all part of a broader effort by the drug industry to join forces with the medical establishment to reduce use of antibiotics, as resistant superbugs become more prevalent in hospitals, nursing homes and other public spaces. Weaning animals from antibiotics in favor of vaccines has become central to that effort. Farm animals are fed about 80 percent of the antibiotics in the U.S., which make their way into the human body....Scientists say there is an intimate link between the health of the planet’s livestock and the human population.

...Farmers and ranchers aren’t eager to give up antibiotics because the drugs are cheap and easy to administer. But change is coming as voluntary Food and Drug Administration rules become mandatory in January....The deadline has prompted the $30 billion animal-health and drug industry to embark on a campaign to educate agribusiness and farmers that vaccines can do just as credible a job protecting animals....A 2015 study estimated the global animal-vaccine market will be worth $7.2 billion by 2020, up from $5.5 billion in 2010.

...The company expects European approval to market Clynav, a DNA vaccine for north Atlantic salmon to fight pancreas diseases. The company is also working on a new vaccine for bovine respiratory disease, ....regulators granted the company a conditional license for its vaccine to help prevent disease caused by avian influenza H5N1 in chickens....Merck Animal Health, also in New Jersey, last year introduced Porcilis Ileitis, a vaccine for bacterial intestinal infections in pigs...“The future of our company is heavily grounded in vaccine development,”...

Here are just a few examples of what you won't read from the pharmaceutical companies:

▲ The administration of live vaccines to animals destined for the human food supply may result in human exposure to a vaccine strain. Illness subsequent to such an exposure is unlikely to be recognized by the patient or the physician as a potential consequence of an animal vaccine exposure. 

▲ ... a chicken virus that represents one of the deadliest germs in history breaks from this conventional wisdom, thanks to an inadvertent effect from a vaccine. Chickens vaccinated against Marek’s disease rarely get sick. But the vaccine does not prevent them from spreading Marek’s to unvaccinated birds. In fact, rather than stop fowl from spreading the virus, the vaccine allows the disease to spread faster and longer than it normally would, a new study finds. The scientists now believe that this vaccine has helped this chicken virus become uniquely virulent.  

▲Situations can be envisioned where potential genetic exchange between certain live vaccines and circulating viruses might be of concern. For example, the use of a live influenza virus vaccine bearing one or more gene segments from a highly pathogenic strain of avian influenza virus has the potential to introduce these genes into other circulating human viruses by reassortment. The use of an attenuated version of the severe acute respiratory syndrome coronavirus as a vaccine might result in recombination with circulating animal or human coronaviruses to create novel mosaic viruses.

▲ Influenza A viruses are highly infectious respiratory pathogens that can infect many species. Birds are the reservoir for all known influenza A subtypes; and novel influenza viruses can emerge from birds and infect mammalian species including humans. Because swine are susceptible to infection with both avian and human influenza viruses...both human and veterinary research needs to give more attention to potential cross-species transmission capacity of influenza A viruses.

If you think you can escape this coming change by buying organic meats, it appears that currently is not the case:

GMO Vaccines Are Used On Organic Livestock 

The USDA National Organic Program “identifies all vaccines, as a group, as synthetic substances allowed for use in organic livestock production. Vaccines are not individually listed on the National List, but rather are included on as a group of synthetic substances termed “Biologics Vaccines,” that may be used in organic livestock production.”

What I keep trying to say in most of my articles is put well here, in these two quotes from separate studies.  Let's hope that the next administration truly is looking out for the welfare of our MICROBIOME:

Modern changes in lifestyle, including improved sanitization, cesarean sections, antibiotic usage, and immunizations are among some of the factors that can shift the microbiota, and are being studied as potential drivers of the sudden increase in immune-mediated diseases in the developed world. 

Moreover, it has recently become obvious that alterations of these gut microbial communities can cause immune dysregulation, leading to autoimmune disorders...........Antibiotic treatments, vaccinations and hygiene practices all can alter gut microbiota composition. 

Teresa Conrick is Contributing Editor to Age of Autism.