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Good Health Depends on Your Bacterial Ecosystem



There are 7 billion humans on planet Earth today with each one of us a walking ecosystem.[*][*]

It is difficult to comprehend that the majority of cells in the human body aren’t even human – with bacterial cells out numbering human cells 10 to 1.[*]

Micro-organisms reside in (just about) every part of our bodies. With over 100 trillion (yeah, with ‘t’) bacteria, these teeny single-celled organisms account for nearly five pounds of our bodily make-up. Our mouth alone is comprised of several hundred species of bacteria – each tooth with its own mini-ecosystem.[*][*]

Scientists (within a multitude of disciplines) equate the bacteria inhabiting the human body as another functioning organ - providing vital tasks critical for human survival.[*][*]



Our Vital Relationship with Bacteria


The science on the critical function of microbes in human health is in its infancy.

What we do understand is that in healthy bodies, bacteria does not cause disease – instead, they coexist in synchronization with their host.[*]

One example among of many, staphylococcus aureus (with several strains linked to the drug-resistant infection called MRSA) can be found in the noses of about 30% of healthy people not causing any illness.[*]

And although bacteria has been seen as the bane of human existence for last century, the knowledge that is accumulating is increasingly viewing them as our fundamental life partners.[*]

Researchers working on the Human Microbiome Project (HMP) report that microbes in our body contribute more genes that are responsible for human survival than humans contribute. Our human genome carries approximately 22,000 genes, while the micro-organisms residing inside us contribute 8 million unique protein genes (360 times more then the human host).[*] 

The genes that are contributed by bacteria are critical, not just for our health, but our survival. For example, bacteria located in our GI-tract contain genes that allow humans to digest AND absorb nutrients that would otherwise be unavailable. Other microbes produce valuable compounds such as vitamins and anti-inflammatories (which regulate some aspects of our immune response, such as swelling) that our genome cannot manufacture.[*]

The old belief that these microbes are freeloaders or invaders is quickly vanishing and being replaced by a new holistic understanding of health.

There are several papers already published, and many more in process, that are drawing the first links between our bacteria and common ailments like irritable bowel syndrome (IBS), unexplained fever in children, obesity, depression, asthma, even ache. Scientists are even attempting to understand how our bacterial makeup contributes to chronic conditions such as cancer and possibly autism.[*][*]


The Significant Origins of a Bacteria Fingerprint


Method of Birth
When we are in our mother’s womb, our gut and body is sterile of bacteria and microbes. Each sterile newborn born vaginally encounters their first exposure to the make-up of their microbial world by means of what their mother is has been exposed to during her life (environment/diet/pets/antibiotics/etc) via the vagina. This event plays a primary role in training the immune system to distinguish ‘good’ bacteria from ‘bad bacteria. Babies that are born surgically via cesarean obtain a different encounter during birth which is fundamentally different from their counterparts which confers a predisposition to food allergies and asthma later in life.[*][*][*][*][*][*][*][*][*]

Although cesarean surgery is necessary for a small amount of pregnancies, it is very much clear that medical reasons alone cannot justify why more then one in three women in America require major abdominal surgery to give birth safely.[*]


Breast milk versus Artificial Supplement 
After a child’s birth there are certain bacterial components, particularly in the intestinal tract, that are deficient and underdeveloped. There is a fixed amount of time to develop an infant’s internal flora properly.[*]

Breast milk, not any other artificial supplement on the market, fosters the colonies of beneficial microbiotic flora that assist with nutrient absorption (particularly iron) and immune system development (specifically sIgA in the first 30 days of life).[*][*]

The distinctive bacterial fingerprint that a breastfed infant has lowers the incidence of diarrhea, influenza and respiratory infections while also providing protection against the later development of allergies, type 1 diabetes, multiple sclerosis and other illnesses.[*][*][*][*][*]

Once past infancy, the composition of the mother’s milk changes according to the child’s specific needs-in fact, the composition of breast milk changes not only daily but hourly! While the time between feedings become longer, the mucosal and bacterial protection continues long after that nursing session is over.[*][*]

An infant’s diet early in life definitely affects his/her individual microbial fingerprint.[*]

The World Health Organization (WHO) states exclusive breast milk is the best food for a newborn, and should not be substituted, since it meets all the child's physiological requirements during the first six months of life (with continued breastfeeding along with appropriate complementary foods up to two years of age or beyond).[*][*]


Anti-bacteria Assault  

According to the CDC, 18 million courses of antibiotics are prescribed for the common cold every year…with an additional 50 million courses prescribed for viral respiratory infections.[*]

It is worth noting that in some of these cases, the prescription is medically warranted – however, the CDC estimates that 80% of the cases it is NOT.[*]  

There are over 10 million antibiotic prescriptions given to children. Every. Year.[*]  

Numerous studies confirm that the use of antibiotics modifies the bacteria in our bodies, some contend that this can last for 6 months, a year, and some even say permanently.[*][*][*]

Obviously, the short term effect of this modification is welcomed (to eliminate unwanted, harmful bacteria), however there are often unwelcome side effects. Particularly in children, adverse consequences experienced can range from diarrhea to abdominal pain. A few studies have even reported higher instances of irritable bowel syndrome, asthma, repeat ear infections and type 1 diabetes.[*][*][*]  

Some of the most popular antibiotics prescribed even come with an infamous black box warning – causing tendon rupture or, most recently, having the ability to block neuromuscular activity (causing fibromyalgia-like symptoms).[*][*]

What is extremely disheartening is that patients (and parents) are rarely informed of the risks associated with antibiotic use (especially repeat use).

And when it comes to doctors, not all are created equal. Those of who have been in practice longer, have a larger patient base and have trained outside the US or Canada are much more likely to prescribe antibiotics inappropriately. For every year a doctor has been in practice, the rate of improper prescribing increases 4%![*]


The key to responsibly using antibiotics:[*]

Ask what antibiotic is being prescribed
Ask if there is an effect alternative
Ask what side effect you should be alert for
Ask when you should expect the unwanted condition to resolve
Ask when you should call is something unexpected happens or if recovery seems delayed
 


Conclusion


We need to become more aware of our symbiotic relationship with the bacteria within the body. This starts with not stereotyping all bacteria as bad. In fact, although a few may be problematic, these account for far less than 1% that exist in our body.[*]

Bacteria are our allies. Our evolution and existence depend largely due to the relationship that has been maintained and preserved for centuries.

They are essential to basic bodily functions: digesting food, producing vitamins, aiding immune response, sustaining good health.[*]

Take care of your ecosystem – it sure takes care of you!




To start learning more, check out: NIH Human Microbiome Project Website

Putting the Herd (Immunity Debate) to Rest

Understanding infectious systems (and debating them) requires a person to be able to reason about highly complex biological structures, of which, contain hundreds of demographic and epidemiological variables.[*]

It seems commonplace in debates/discussions concerning herd immunity that extrapolating demands on others are made – particularly to maintain specific elimination thresholds (one example easily comes to mind: non-medical vaccine exemptions should be void to maintain herd immunity). 


Elimination Thresholds and the Dynamics of Immunity

Two authentic hazards arise when debates concerning herd immunity/vaccination rates place consistent emphasis on maintaining elimination thresholds (ie 90-95% vaccination rates)

(1) the debate begins to distract from the fundamental extreme dynamics of epidemic theory, particularly to herd immunity[* pg297]  

(2) the debate portrays a human life as a instrument in medicine that can/should be utilized in a societal defense against viruses/bacteria/disease. (the dismissal pertaining to an individual’s choice regarding a medical procedure)


For this post, I will only be addressing the first point (the complexities relating to the influences on herd immunity). To learn more about the second issue you can read this post.

I feel the need to address this particular point because in common debates regarding herd immunity (pertaining to national vaccination programs) a fundamental cornerstone of epidemiology is continually dismissed: the extreme dynamic consequences of the intrinsic nonlinearity of host-agent systems.[*] 

In laymens terms – this shit is complex.


Does Herd Immunity Exist?

Absolutely.

There is no denying that herd immunity is an extremely potent natural phenomenon which is altered by a multitude of influences (which I am going to attempt to list briefly a little later). In the presence of a national vaccine program, it is purposefully manipulated with the intention that the recognized gains will out weigh any known disadvantage(s) that might occur (financially, safety, policy, etc). [*]

In the United States, we rely on the ACIP to examine new (and current) vaccination campaigns of which must be weighed very cautiously. To intentionally modify the current existing herd immunity against a non-fatal, acute childhood disease can carry unfortunate characteristics such as protecting one population while actually placing another group at higher risk than before (ex varicella campaign).[*][*][*][*]


On the other hand, there are campaigns that historically have provided success. So far, the only infection to be eradicated worldwide is smallpox (variola major -WHO 1977). This accomplishment generated much optimism in the philosophy of eradication thresholds that other infectious diseases (such as measles and pertussis) were targeted.  Unfortunately, this thinking may have been misguided for many reasons: smallpox was unique given its low communicability, the high average age of infection, the ease of diagnosis and the stability of vaccine storage conditions.[*]


It is also important to reveal, that there are complete absences of herd immunity seen in several diseases (some of which we currently vaccinate against such as rubella, diphetheria, pertussis).[*]

The blanket justification of herd immunity in support of elimination thresholds for vaccination on the current US vaccine schedule has the very real potential in becoming a crude and one-dimensional debate.


The Fundamentals

When speaking of herd immunity in relationship to a national vaccination campaign, one must be specific to which disease they are discussing and they must show an understanding to the intricate nature of influences of immunity within the individual and within a community.

To begin, a foundation must be understood. Epidemic theory considers three variables: agent, host and environment (each of which has many components/interactions/influences in-and-of themselves).

Agent
An agent is any infectious pathogen. These vary in biological makeup, size, transmission, and habitat. In the construction of mathematical models of epidemics and herd immunity, all possible variations in all aspects of the agent's behavior (particularly in relation the host and the environment) must be taken into account.[*]

Host
The classification of a host is relevant when an agent invades a foreign entity (aka the host) resulting in a defensive immune response with the purpose of protection. Immunity attained can range from temporary to permanent. [*] 


What is of particular study is the host’s response with antibodies specific to the infectious antigen. These seropositive individuals are those who have current infections or who have experienced an infection in the past – moving them from the category of ‘infected’ to ‘recovered’.[*]    

Of course, when referring to the context of herd immunity, one must consider both the individual hosts and the population as a whole.


Environment
Consideration and concern is given to the environment and vicinity in which both the host and agent dwell. This can range from geographical heterogeneity to seasonal variations (again, for both host and agent).



Mathematical Modeling – SIR Model

Epidemiology gives birth to herd immunity theory when the first mathematical model examined how infectious agents affected large populations over time.[*][*][*]

Obviously, for ethical reasons and financial reasons (hopefully the former out weighs the later), experimentation or field trials are prohibitive – making mathematical modeling critical in making theoretical predictions of how a disease will spread and can be useful for evaluating control strategies (particularly in the case of a bio-weapon attacks).[*][*]

The Mass Action Principle (SIR) has been widely applied and accepted in epidemic theory since 1927 – when Kermack and McKendrick published 3 papers outlining and describing a mathematical model in which they considered a fixed population with 3 compartments: susceptible; infected; recovered (SIR).[*][*][*]


Susceptibles (S) – Individuals that are susceptible have, in the case of the basic SIR model, never been infected, and they are able to catch the disease. Once they have it, they move into the Infected compartment.[*]

Infected (I) – Infected individuals can spread the disease to susceptible individuals. The time they spend in the infected compartment is the infectious period, after which they enter the recovered compartment. [*]

Recovered (R) – immune to the disease or otherwise removed from the population. Individuals in the recovered compartment are assumed to be immune for life. [*]


In the SIR model, vaccination is equivalent to complete removal (aka transfer to the Recovered compartment). It is assumed that vaccinated individuals can not infect or be infected. [*] 

The above described SIR model is helpful although it is written using an equation that implies a deterministic model (no randomness with a continuous time). [*]

To account for this, the SIR model is the basis for other similar models (SEIS, MSIR, MSEIRS) that make small adjustments in its parameters that attempt to alleviate certain ‘real-world’ problems, for example:[*][*] 

SEIS  - considers the exposed or latent period of the disease (a person is not immediately infected).

MSEIRS – considers an infection that does not leave a lasting immunity in which individuals that have recovered will return to being susceptible again, moving back into the S compartment.

MSIR – considers a disease where an individual is born with a passive immunity from the mother.


Although mathematical equations are very useful in understanding basic principles and the interplay between variables, their assumptions can lead to oversimplification.[*][*]

My concern centers on the simplicity of many mathematical models, particularly in the face of such biological complexity. Especially useful tools in modern complex theories incorporate multiple algorithms and concepts of TCS (theoretical computer science), however these tools are not yet utilized and relatively unknown in epidemiology.[*][*]



Complexities of the Herd

There are several assumptions made in the formulation of the above mentioned equations. These assumptions have benefits and disadvantages.

Benefits may include being utilized for a general guide to risk assessment or a supportive piece to compare alternative policies/intervention – a wide-ranging compass to help make epidemiological decisions.

However, it is clear that to make the forecast more realistic, it is necessary to introduce more details in the disease dynamics. Models that incorporate even the most elaborate derivations omit important features.[* pg 296]

Here are a handful of features to begin to take into consideration that influence the dynamics of disease, immunity, transmission, and recovery.[*]


Geographical heterogeneity
This refers to gender (i.e. male-female ratios), age, and factors correlated with residence. Because of existing heterogeneity, estimated elimination thresholds vary between local communities – significant local differences in population dynamics arise which, consequently adjust estimates.[*][*]

Areas of similar dynamics and variation pertaining to heterogeneity:

• Age-Structured populations
• Variable infectivity
• High contact probabilities
• Persistence of pathogens within hosts
• Variations in infection risk by age group
• Limitation of application to a closed population (no immigration or emigration)[*]
• Demographic turnover (birth or death).[*]


Host genetic factors
A particularly new dynamic gaining more comprehension is the role of host genetic factors – this dynamic is critical because mathematical models rely on and individual within the population as having an equal probability as every other individual of contracting and transmitting a disease.[*][*][*]

Research is continuing to learn strategies to identify host genes responsible for resistance/susceptibility to particular agents and the relationship between vaccine efficacy and genetics.

Areas of similar dynamics and variation pertaining to host genetic/immuno factors:

• intra-host dynamics
• Maternal immunity


Spatial epidemiology
The most fundamental of these is the problem of defining the spatial location of the entities being studied. For example,

In regards to the study on human health, spatial position of humans can pertain to the area or point with where an individual/group live, or with a point located where they work, or by using a line to describe their weekly trips. Each variation has dramatic effects analysis and on the conclusions obtained.[*]

Other issue arise in the application of spatial analysis which includes the limitation of mathematical knowledge problems in computer based calculations.[*] 


Antigenic shift
Antigenic shift is contrasted with antigenic drift (a natural mutation over time). The issue with antigenic shift concerns our lack ability to forecast ability of viruses to alter their genetic makeup (quickly creating mutant antigens) and bypassing the antibody barrier a host/community.[*]


Phylodynamics
Viral phylodynamics examines how epidemiological, immunological, and evolutionary processes impact viral genetic variation.

Dynamics of transmission is considered at the level of cells within an infected host, individual hosts within a population, or entire populations of hosts.[*]

Currently, it is understood that viruses within similar hosts, such as hosts that reside in the same geographic region, are expected to be more closely related genetically if transmission occurs more commonly between them.[*]

Areas of similar dynamics and variation pertaining to phylodynamics:

• pathogen population genetics
• evolution and spread of resistance to immunity/medication
• Strain (biology) structure and interactions


Seasonal variations
There are several biologically distinct mechanisms in which seasonality and climate change impacts host-pathogen interactions. Strong pressures on population dynamics are exerted by temperature, rainfall, seasonality and climate change – responses can range from simple annual cycles to more complex multiyear fluctuations.[*][*]

Although scientists are only beginning to understand how seasonal external drivers influence the majority of host–parasite systems, empirical evidence strongly supports the strength and mechanisms of which seasonality alters the spread and persistence of infectious diseases. [*][*]

To present two examples for further understanding:

Agent: rotavirus.
Seasonal affects: winter peaks; timing shifts with latitude[*]

Agent: meningococcal meningitis
Seasonal affect: wind speed and low humidity affect respiratory/aerosol transmission[*]

Areas of similar dynamics and variation pertaining to seasonal variation:

• alterations in immune system defenses (weakened during winter and during harsh weather)
• periparturient rise (pregnant women lowering their own immunity to prevent harming the fetus)
• diseases that are cyclical in nature
• diseases that are seasonal in nature



Ending the Debate on Herd Immunity 

Agent-Host-Environment: This relationship is complex and depends on such factors as a precise course of infection (not only with an individual but within the demography of the host population). Other factors include duration of immunity (natural or artificially acquired), maternally derived protection, age-related changes in the intimacy of contacts – not to mention a prevailing level of genetic and spatial heterogeneity in both susceptibility and resistance to infection.[*]

There is no denying that mathematical models aid in defining details associated with infectious systems. Adjustments made to incorporate dynamic influences have the ability to make useful generalities and estimates – particularly to elimination thresholds and the course of infection within a population.[*] 

However, the science and intuition built on decades of practical epidemiological experience still often fail to predict outcomes/implications of vaccination programs.[*]

Each vaccination campaign entails a massive disruption of the previous balance which results in a destabilization of epidemiologic patterns for many years.[* p297]

...are vaccinated individuals the ones stepping outside the herd?

Herd immunity existed prior to vaccination.

Preceding national vaccination programs, epidemiological patterns of immunity/disease existed for the greater good. With each national vaccine campaign, epidemiology is modified (benefiting some and disadvantaging others).

While it is perceived beneficial that some vaccinated diseases have diminished over time (such as measles, chicken pox, rubella), it is very likely that these infections existed in a precise biological niche that was very much intentional – benefits in which our understanding can not yet comprehend.[*]

How exactly can the herd immunity debate end? 

(1) Accepting that the encompassing complexity of infectious disease (and nature in general) is not something human understanding will be able comprehend in entirety. Yes, artifical modification (via vaccine) can impart benefits – but it also exposes populations/individuals to disadvantages (many of which cannot be forecasted in advance) – implementation of vaccine programs must not be taken lightly nor forced upon a population without individual consent. 

(2) Above all else, voluntary consent married with adequate comprehension of each vaccine is fundamental as national vaccine campaigns develop and progress. This is whatshould be the underlying principle in discussions on herd immunity – NOT mandatory vaccination.



This post is dedicated to those families that have been deliberately and maliciously accused of ‘free riding’ off of vaccine-induced/artificial herd immunity – especially those who have been told this by a medical professional in hopes of altering a consent of vaccination.

I like to believe all parents are doing the best they can. Please choose what works best for your family while honoring the rights of others to make that same choice.

Alternatives to Chemical Lawn Treatments



You know what really grinds my gears?

Lawn chemicals being advertised as grass “food”.

Let’s call a duck a duck. Herbicides and pesticides (aka lawn chemicals) are formulated for one purpose and that’s basically to kill everything on your lawn, except grass.

When did sacrificing the health of homeowners, their families, pets and all other forms of life become okay for the attainment of a weed-free lawn?

Grrr. That imaginary property line does NOT contain your pestcidal drift, my dear neighbor.

Lawn chemicals are readily inhaled, tracked inside the home and absorbed though the skin. The National Academy of Sciences report that at least 1 out of 7 people are significantly harmed by pesticide exposure. The chemicals used on lawns can cause coughing, muscle pain, sleep disorders, fatigue, etc – with long term documented consequences of lowered fertility, immune disorders, and cancer.[*]


“Of 30 commonly used lawn pesticides, 19 are linked with cancer or carcinogenicity, 13 are linked with birth defects, 21 with reproductive effects, 26 with liver or kidney damage, 15 with neurotoxicity, and 11 with disruption of the endocrine (hormonal) system. Of those same pesticides, 17 are detected in groundwater, 23 have the ability to leach into drinking water sources, 24 are toxic to fish and other aquatic organisms vital to our ecosystem, 11 are toxic to bees, and 16 are toxic to birds.” [*]


Using chemicals on grass in hopes to achieve a ‘weed-free’ lawn is completely absent of logic. Chemicals kill earthworms and other living organisms that live in the ground that help grow grass. Lawn chemicals also add salt and changes the pH of the soil which aids in breeding of harmful insects.[*]

Where is the logic in this?

The grass, soil and the eco-structure of the lawn wholly changes and becomes reliant on more and more chemicals to maintain the artificial eco-configuration. In all actuality, the chemicals used on grass over a long period of time can actually help the very pests they target by eliminating their predators – making their use self-perpetuating.

Good for lawn chemical businesses – not so good for your grass (or your health).


But don’t fret, I’ve been reading and learning more about how to maintain a healthy lawn, free of weird synthetic chemicals, because my husband is adamant about how our grass looks.

So here is to the lawn-conscious husbands (and wives).

There are a lot of things you can do to create a more beautiful lawn. Although, a completely weed-free lawn is not enterly practical, you can get very close without the use of nasty chemicals.

First, you need to think of weeds as a symptom of other problems. You have to adjust the current conditions (such as compacted soil, too wet/dry areas, shady spots, mowing too low,etc) to reduce weeds.[*]

Most of the following would be fun to do with kids too – and would provide a great opportunity to teach them about how we are all interconnected with the planet!


Mow high.
Mowing too low places stress on grass plants and exposes growing weeds to sunlight. Let the grass grow a little – who wouldn’t like this tip?

Plant worms.
Planting earthworms are hugely beneficial to grass. Worms provide free fertilizer, aerate soil and even eat cur grass.

Refrain from watering.
During certain dry periods, allow the grass to enter its natural dormancy…and give the pocket book a little breather.

Dandelions.
It’s good to cut these particular weeds out by hand at the root. Get some vitamin D, and put the kids to work collecting dandelions.

Aerate.
Compacted dirt will promote weeds. Aerate your lawn twice a year and plant grass which will choke out weeds (pick varieties that are resistant to drought and need little mowing).