21. Appl Environ Microbiol. 2012 Nov;78(21):7626-37. doi: 10.1128/AEM.02036-12. Epub
2012 Aug 24.
Yergeau E(1), Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR, Greer CW.
(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.
PMID: 22923391 [PubMed - indexed for MEDLINE]
22. J Microbiol Biotechnol. 2013 Apr;23(4):459-66.
Prajapati JB(1), Nathani NM, Patel AK, Senan S, Joshi CG.
(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.
Jackson CR(1), Millar JJ(2), Payne JT(2), Ochs CA(2).
(1)Department of Biology, The University of Mississippi, University, Mississippi,
USA firstname.lastname@example.org. (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.
PMID: 25217018 [PubMed - indexed for MEDLINE]
24. MBio. 2014 Oct 7;5(5):e01580-14. doi: 10.1128/mBio.01580-14.
Bisanz JE, Enos MK, Mwanga JR(1), Changalucha J(1), Burton JP, Gloor GB(2), Reid
(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.
PMID: 25293764 [PubMed - indexed for MEDLINE]