High-throughput microbial gene detection seems like the future? - and technology used to identify dysbiosis, gut-brain connection
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TOPIC: High-throughput microbial gene detection seems like the future? - and technology used to identify dysbiosis, gut-brain connection

Sanitation is not yet commonly associated with global obesity epidemics - should it be? 12 Apr 2014 02:13 #8211

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    KeithBell
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Small islands are closed systems, microcosms of the planet.

This documentary details the challenges of small island sanitation:


I find it especially interesting how this combination of poor sanitation and the traditional root vegetable diet of the Pacific Islands has resulted in the world's highest rates of obesity. Root vegetables are very high in resistant starch possibly feeding an overgrowth of Firmicutes intestinal bacteria associated with obesity, diabetes and heart disease. This would occur over generations such that children are born predisposed to obesity, a matter of microbial predisposition. Sanitation is not yet commonly associated with global obesity epidemics, but I wonder if poor sanitation is a major factor in obesity epidemics, i.e., Persian Gulf nations.
en.wikipedia.org/wiki/Obesity_in_the_Pacific

We have the exact challenges here in Florida, USA as we pollute important coastal waters with septic waste and nutrient-laden water discharges from Lake Okeechobee. The Indian River, for example, is in peril for these reasons. I'm presently on a team having notified Florida Department of Health of a lawsuit claiming they have violated the Endangered Species Act in allowing septic waste to threaten the Indian River Lagoon (IRL). Here's our website; my input including links is under Re-Plumbing the Future:
www.manateeindianriverlagoon.com/

A nice piece of environmental journalism on the IRL issue:
creative.news-journalonline.com/troubledwater/

Thanks for reading, I hope you enjoy the documentary!
Last Edit: 12 Apr 2014 02:17 by KeithBell.

High-throughput microbial gene detection seems like the future? - and technology used to identify dysbiosis, gut-brain connection 07 May 2014 20:57 #8517

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    KeithBell
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Note by moderator: The first 7 posts in this thread were originally in this thread on "a better way to test pathogen inactivation":
forum.susana.org/forum/categories/26-hea...dsource-a-better-way
But they fit better into this separate thread.

++++++++++


High-throughput microbial gene detection seems like the future; here's food for thought, 2013:
Detecting Human Bacterial Pathogens in Wastewater Treatment Plants by a High-Throughput Shotgun Sequencing Technique

pubs.acs.org/doi/abs/10.1021/es400275r (full paper attached below)

Given mycobacterium tuberculosis found in "high abundance" in sludge and effluent, I'm not sure why TB isn't considered a waterborne disease. Experts still believe it's all about airborne transmission.
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Last Edit: 23 Jul 2014 22:16 by muench.

Re: Wanting a better way to test pathogen inactivation? Us too! Can you help me crowdsource a better way? 08 May 2014 08:24 #8523

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    PatrickBBB
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  • Water and environment engineer.
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Very interesting Keith, all though I do not think it is what the original poster (OP) was looking for.

The article states:
However, it is worth noting that such a molecular technique is difficult to exactly quantify pathogens in terms of cell number in influent, activated sludge, and effluent because of the high complexity to convert gene copy number to cell number.

Unfortunately it does not say how accurate it can be, but as Joe pointed out earlier in this thread; what's interesting is the pathogen concentration. (In order to conduct a QMRA) Could you explain what the article means by pathogenic bacteria relative abundance?

I also identified some other constraints to the method.

- It requires very expensive equipment (the sequencer used in this experiment was prized at 690000 USD when it was released in 2010)
- It requires a lot of competence.
- All though it does not specifically say it, I assume it requires a lot of time.

Also, what I want to see are real-time sensors that can monitor the microbial effluent (and influent in the case of a DWTP) quality. Light scattering seems more promising in this regard in my opinion.
Happy learning.
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Re: Wanting a better way to test pathogen inactivation? Us too! Can you help me crowdsource a better way? 23 May 2014 16:37 #8713

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    KeithBell
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Patrick, I'm still learning about how this technology can and will be applied to sanitation. Pricing of the technology has become much more affordable and testing is very fast.

Modern day hero, environmental microbiologist, Dr. Rita Colwell uses molecular techniques. Here's a recent presentation with focus on cholera:


Here's Dr. Colwell's most recent paper published a few days ago about microbial communities in saliva:
Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing
www.plosone.org/article/info%3Adoi%2F10....journal.pone.0097699

General papers; I believe this kind of work can now be done on a laptop:
www.plosone.org/article/info%3Adoi%2F10....journal.pone.0060811
www.ncbi.nlm.nih.gov/pubmed/20566210
www.plosone.org/article/info%3Adoi%2F10....journal.pone.0079490
www.plosone.org/article/info%3Adoi%2F10....journal.pone.0076185
link.springer.com/article/10.1007%2Fs00253-012-4082-4

Re: Wanting a better way to test pathogen inactivation? Us too! Can you help me crowdsource a better way? 20 Jul 2014 17:58 #9416

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    KeithBell
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Here are two very recent papers sanitation professionals should be interested in as they may help to determine indicator species and also talk about technology used to identify dysbiosis:

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition
genomebiology.com/2014/15/6/R76

MALDI-TOF Identification of the Human Gut Microbiome
in People with and without Diarrhea in Senegal

www.plosone.org/article/info%3Adoi%2F10....journal.pone.0087419
In individuals with diarrhea, major commensal bacterial species such as E. coli were significantly decreased (85% versus 64%), as were several Enterococcus spp. (E. faecium and E. casseliflavus) and anaerobes, such as Bacteroides spp. (B. uniformis and B. vulgatus) and Clostridium spp. (C. bifermentans, C. orbiscindens, C. perfringens, and C. symbosium). Conversely, several Bacillus spp. (B. licheniformis, B. mojavensis, and B. pumilus) were significantly more frequent among patients with diarrhea.


Here's some press about the recent study posted above:
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

"Scientists Identify New Microbes Associated with Severe Diarrhea"
cmns.umd.edu/news-events/features/2305

"Previously Unheralded Microbes Cause And Prevent Severe Diarrhea"
www.science20.com/news_articles/previous...vere_diarrhea-139500

Note: what causes diarrhea in one population may be different from another as flora balance varies considerably, i.e., European vs. African, the underlying beauty of diversity.
Last Edit: 24 Jul 2014 15:55 by KeithBell.

Re: Wanting a better way to test pathogen inactivation? Us too! Can you help me crowdsource a better way? 22 Jul 2014 09:10 #9430

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    joeturner
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  • Science Journalist - but rarely about sanitation.. all views and errors mine
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Interesting, but irrelevant Keith.

The issue is this: we cannot measure directly all of the microbial pathogens in faecal waste hence the need for a reliable indicator that we can measure which models the breakdown of all the pathogens that we cannot measure.

What these papers seem to be showing is the gut flora of people with and without diarrhea in Senegal - and have found a measurable difference between groups.

This is essentially descriptive. I don't think they are saying that one could analyse faecal waste and use this suite of species to tell whether pathogens have been destroyed. But even if they are saying that, it still is not very helpful because you would have to be able to plate out lots of different microbes, which is expensive and not really the point of an indicator.
Previously trained and worked as a Soil Scientist and worked on projects composting sewage sludge.
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Gut dysbiosis/malabsorption syndrome is rampant due to poor sanitation 21 Dec 2014 18:19 #11439

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    KeithBell
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Note by moderator: This post was originally in this thread but has been moved to here to keep the other thread more focussed.
+++++++++++++


Susannah, the "hygiene hypothesis" doesn't hold much weight in view of high rates of infant and maternal mortality now associated with poor sanitation. Gut dysbiosis/malabsorption syndrome is rampant due to poor sanitation, finally being acknowledged in mainstream media.

But I still like your point and believe we should also focus on how a toxic, polluted environment shifts flora in the wrong direction and out of balance.

Here's a 2014 study about organic pollutants in septic waste (not about pathogens):
Pharmaceuticals, perfluorosurfactants, and other organic wastewater compounds in public drinking water wells in a shallow sand and gravel aquifer.
www.ncbi.nlm.nih.gov/pubmed/24055660
Septic systems appear to be the primary source of OWCs in Cape Cod groundwater, although wastewater treatment plants and other sources were potential contributors to several wells.
Last Edit: 22 Dec 2014 15:06 by muench.

Re: Gut dysbiosis/malabsorption syndrome is rampant due to poor sanitation 22 Dec 2014 15:39 #11446

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    KeithBell
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Here's a new article along with two new open access papers regarding infant and maternal mortality and poor sanitation:
A matter of birth and death: unsafe conditions still killing new mothers and newborns
www.lshtm.ac.uk/newsevents/news/2014/matter_birth_death.html

The companion paper about Tanzania is interesting as I've recently learned about the Hazda people of Tanzania practicing open defecation while suffering high infant mortality rates. This is somewhat counterintuitive since the Hazda are famously studied for their diverse intestinal microbiomes and ancestral diet associated with good health (lack of chronic illness seen in developed nations). There are currently no efforts I'm aware of to improve sanitation. Instead, the Hazda are beginning to submit to vaccination, a grand experiment which may lead to injuries.

And here we have another new paper about maternal and reproductive health:
Getting the basics right – the role of water, sanitation and hygiene in maternal and reproductive health; a conceptual framework
onlinelibrary.wiley.com/doi/10.1111/tmi.12439/abstract
It's good to see focus on this issue from a microbial standpoint as the womb has previously and wrongly been considered a sterile environment, a fallacy promoted in peer-reviewed papers without evidence for decades.

Lastly for now, this recent NYT article (also posted in a thread here about antibiotic resistance) where it's surmised infant mortality associated with poor sanitation is a matter of microbial prediposition where microbes are transmitted from mother to child in the birthing process, though placental transmission should be the concern.
‘Superbugs’ Kill India’s Babies and Pose an Overseas Threat
www.nytimes.com/2014/12/04/world/asia/su...eas-threat.html?_r=0
Last Edit: 22 Dec 2014 15:48 by KeithBell.

Re: Malnutrition’s Links to Sanitation in India - and Wikipedia pages on stunting, helminthiasis and EE 14 Feb 2015 19:48 #12060

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    KeithBell
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Here's a new PBS article with moving collection of photos:
www.pbs.org/newshour/updates/in-worlds-p...a-childs-playground/

The text of the article is mainly about sanitation while most of the photos seem to convey solid waste issues. Perhaps it's difficult to communicate the problem of poor sanitation leading to malabsorption syndrome in photos.

Regarding tropical sprue, there appears to be much overlap in the medical literature with now rampant gut diseases such as IBS and Celiac disease, where Celiac disease now affects one in 100 people in the developed world.
www.nature.com/ajg/journal/v108/n5/full/ajg201345a.html
www.ncbi.nlm.nih.gov/pubmed/22315745

The problem may be that Celiac disease was once predominantly considered of genetic origin, but that's changing rapidly where the field is finally embracing probiotic therapy when it was shunned in the past. The only treatment until recently was the gluten-free diet which can actually feed the problem based on high sugar. Recent studies now confirm gut dysbiosis including abundance of Proteobacteria (E. coli, Klebsiella, etc.) in Celiac disease.
www.ncbi.nlm.nih.gov/pubmed/23478804
www.nature.com/ajg/journal/v109/n12/abs/ajg2014355a.html
www.cureceliacdisease.org/who-we-are/video (first video, The Celiac Microbiome Research Initiative)

I tend to doubt Celiac disease is much different than tropical sprue.
Last Edit: 15 Feb 2015 21:54 by KeithBell.
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