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21. Appl Environ Microbiol. 2012 Nov;78(21):7626-37. doi: 10.1128/AEM.02036-12. Epub

2012 Aug 24.


Next-generation sequencing of microbial communities in the Athabasca River and

its tributaries in relation to oil sands mining activities.


Yergeau E(1), Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR, Greer CW.


Author information:

(1)National Research Council Canada, Montreal, Quebec, Canada.


The Athabasca oil sands deposit is the largest reservoir of crude bitumen in the

world. Recently, the soaring demand for oil and the availability of modern

bitumen extraction technology have heightened exploitation of this reservoir and

the potential unintended consequences of pollution in the Athabasca River. The

main objective of the present study was to evaluate the potential impacts of oil

sands mining on neighboring aquatic microbial community structure. Microbial

communities were sampled from sediments in the Athabasca River and its

tributaries as well as in oil sands tailings ponds. Bacterial and archaeal 16S

rRNA genes were amplified and sequenced using next-generation sequencing

technology (454 and Ion Torrent). Sediments were also analyzed for a variety of

chemical and physical characteristics. Microbial communities in the fine tailings

of the tailings ponds were strikingly distinct from those in the Athabasca River

and tributary sediments. Microbial communities in sediments taken close to

tailings ponds were more similar to those in the fine tailings of the tailings

ponds than to the ones from sediments further away. Additionally, bacterial

diversity was significantly lower in tailings pond sediments. Several taxonomic

groups of Bacteria and Archaea showed significant correlations with the

concentrations of different contaminants, highlighting their potential as

bioindicators. We also extensively validated Ion Torrent sequencing in the

context of environmental studies by comparing Ion Torrent and 454 data sets and

by analyzing control samples.


DOI: 10.1128/AEM.02036-12

PMCID: PMC3485728

PMID: 22923391  [PubMed - indexed for MEDLINE]



22. J Microbiol Biotechnol. 2013 Apr;23(4):459-66.


Genomic analysis of dairy starter culture Streptococcus thermophilus MTCC 5461.


Prajapati JB(1), Nathani NM, Patel AK, Senan S, Joshi CG.


Author information:

(1)Department of Dairy Microbiology, SMC College of Dairy Science, Anand

Agricultural University, Anand-388 001, Gujarat, India.


The lactic acid bacterium Streptococcus thermophilus is widely used as a starter

culture for the production of dairy products. Whole-genome sequencing is expected

to utilize the genetic basis behind the metabolic functioning of lactic acid

bacterium (LAB), for development of their use in biotechnological and probiotic

applications. We sequenced the whole genome of Streptococcus thermophilus MTCC

5461, the strain isolated from a curd source, by 454 GS-FLX titanium and Ion

Torrent PGM. We performed comparative genome analysis using the local BLAST and

RDP for 16S rDNA comparison and by the RAST server for functional comparison

against the published genome sequence of Streptococcus thermophilus CNRZ 1066.

The whole genome size of S. thermophilus MTCC 5461 is of 1.73Mb size with a GC

content of 39.3%. Streptococcal virulence-related genes are either inactivated or

absent in the strain. The genome possesses coding sequences for features

important for a probiotic organism such as adhesion, acid tolerance, bacteriocin

production, and lactose utilization, which was found to be conserved among the

strains MTCC 5461 and CNRZ 1066. Biochemical analysis revealed the utilization of

17 sugars by the bacterium, where the presence of genes encoding enzymes involved

in metabolism for 16 of these 17 sugars were confirmed in the genome. This study

supports the facts that the strain MTCC 5461 is nonpathogenic and harbors

essential features that can be exploited for its probiotic potential.



PMID: 23568199  [PubMed - indexed for MEDLINE]



23. Appl Environ Microbiol. 2014 Dec;80(23):7186-95. doi: 10.1128/AEM.01844-14. Epub

2014 Sep 12.


Free-Living and Particle-Associated Bacterioplankton in Large Rivers of the

Mississippi River Basin Demonstrate Biogeographic Patterns.


Jackson CR(1), Millar JJ(2), Payne JT(2), Ochs CA(2).


Author information:

(1)Department of Biology, The University of Mississippi, University, Mississippi,

USA cjackson@olemiss.edu. (2)Department of Biology, The University of

Mississippi, University, Mississippi, USA.


The different drainage basins of large rivers such as the Mississippi River

represent interesting systems in which to study patterns in freshwater microbial

biogeography. Spatial variability in bacterioplankton communities in six major

rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas)

of the Mississippi River Basin was characterized using Ion Torrent 16S rRNA

amplicon sequencing. When all systems were combined, particle-associated (>3 μm)

bacterial assemblages were found to be different from free-living

bacterioplankton in terms of overall community structure, partly because of

differences in the proportional abundance of sequences affiliated with major

bacterial lineages (Alphaproteobacteria, Cyanobacteria, and Planctomycetes). Both

particle-associated and free-living communities ordinated by river system, a

pattern that was apparent even after rare sequences or those affiliated with

Cyanobacteria were removed from the analyses. Ordination of samples by river

system correlated with environmental characteristics of each river, such as

nutrient status and turbidity. Communities in the Upper Mississippi and the

Missouri and in the Ohio and the Tennessee, pairs of rivers that join each other,

contained similar taxa in terms of presence-absence data but differed in the

proportional abundance of major lineages. The most common sequence types detected

in particle-associated communities were picocyanobacteria in the

Synechococcus/Prochlorococcus/Cyanobium (Syn/Pro) clade, while free-living

communities also contained a high proportion of LD12 (SAR11/Pelagibacter)-like

Alphaproteobacteria. This research shows that while different tributaries of

large river systems such as the Mississippi River harbor distinct

bacterioplankton communities, there is also microhabitat variation such as that

between free-living and particle-associated assemblages.


Copyright © 2014, American Society for Microbiology. All Rights Reserved.


DOI: 10.1128/AEM.01844-14

PMCID: PMC4249191

PMID: 25217018  [PubMed - indexed for MEDLINE]



24. MBio. 2014 Oct 7;5(5):e01580-14. doi: 10.1128/mBio.01580-14.


Randomized open-label pilot study of the influence of probiotics and the gut

microbiome on toxic metal levels in Tanzanian pregnant women and school children.


Bisanz JE, Enos MK, Mwanga JR(1), Changalucha J(1), Burton JP, Gloor GB(2), Reid



Author information:

(1)National Institute for Medical Research, Mwanza, Tanzania. (2)Department of

Biochemistry, The University of Western Ontario, London, Canada.



Exposure to environmental toxins is a 21st century global health problem that is

often the result of dietary intake. Although efforts are made to reduce dietary

toxin levels, they are often unsuccessful, warranting research into novel methods

to reduce host exposure. Food-grade microbes that can be delivered to the

gastrointestinal tract and that are capable of sequestering toxins present a safe

and cost-effective intervention. We sought to investigate the potential for

probiotic-supplemented yogurt to lower heavy metal levels in at-risk populations

of pregnant women and in children in Mwanza, Tanzania, and to examine the

microbiome in relation to toxin levels. Two populations suspected to have high

toxic metal exposures were studied. A group of 44 school-aged children was

followed over 25 days, and 60 pregnant women were followed over their last two

trimesters until birth. A yogurt containing 10(10) CFU Lactobacillus rhamnosus

GR-1 per 250 g was administered, while control groups received either whole milk

or no intervention. Changes in blood metal levels were assessed, and the gut

microbiomes of the children were profiled by analyzing 16S rRNA sequencing via

the Ion Torrent platform. The children and pregnant women in the study were found

to have elevated blood levels of lead and mercury compared to age- and

sex-matched Canadians. Consumption of probiotic yogurt had a protective effect

against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3

nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not

statistically significant in the children. Elevated blood lead was associated

with increases in Succinivibrionaceae and Gammaproteobacteria relative abundance

levels in stool. Importance: Probiotic food produced locally represents a

nutritious and affordable means for people in some developing countries to

counter exposures to toxic metals. Further research and field trials are

warranted to explore this approach in countries where communities are located

near mining sites and agricultural areas, two types of areas where toxins are

likely to be elevated.


Copyright © 2014 Bisanz et al.


DOI: 10.1128/mBio.01580-14

PMCID: PMC4196227

PMID: 25293764  [PubMed - indexed for MEDLINE]