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25. Int J Environ Res Public Health. 2014 Feb 21;11(2):2299-313. doi:



Environmental arsenic exposure and microbiota in induced sputum.


White AG(1), Watts GS(2), Lu Z(3), Meza-Montenegro MM(4), Lutz EA(5), Harber

P(6), Burgess JL(7).


Author information:

(1)Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson

85724, USA. (2)Department of Pharmacology and University

of Arizona Cancer Center, Tucson, AZ 85724, USA.

(3)Statistical Consulting Laboratory, University of Arizona, Tucson, AZ 85712,

USA. (4)Department of Biotechnology and Food Sciences, Instituto

Technologico de Sonora, Sonora 85000, Mexico. (5)Mel and Enid

Zuckerman College of Public Health, University of Arizona, Tucson 85724, USA. (6)Mel and Enid Zuckerman College of Public Health,

University of Arizona, Tucson 85724, USA. (7)Mel and

Enid Zuckerman College of Public Health, University of Arizona, Tucson 85724,



Arsenic exposure from drinking water is associated with adverse respiratory

outcomes, but it is unknown whether arsenic affects pulmonary microbiota. This

exploratory study assessed the effect of exposure to arsenic in drinking water on

bacterial diversity in the respiratory tract of non-smokers. Induced sputum was

collected from 10 subjects with moderate mean household water arsenic

concentration (21.1 ± 6.4 ppb) and 10 subjects with low household water arsenic

(2.4 ± 0.8 ppb). To assess microbiota in sputum, the V6 hypervariable region

amplicons of bacterial 16s rRNA genes were sequenced using the Ion Torrent

Personal Genome Machine. Microbial community differences between arsenic exposure

groups were evaluated using QIIME and Metastats. A total of 3,920,441 sequence

reads, ranging from 37,935 to 508,787 per sample for 316 chips after QIIME

quality filtering, were taxonomically classified into 142 individual genera and

five phyla. Firmicutes (22%), Proteobacteria (17%) and Bacteriodetes (12%) were

the main phyla in all samples, with Neisseriaceae (15%), Prevotellaceae (12%) and

Veillonellacea (7%) being most common at the genus level. Some genera, including

Gemella, Lactobacillales, Streptococcus, Neisseria and Pasteurellaceae were

elevated in the moderate arsenic exposure group, while Rothia, Prevotella,

Prevotellaceae Fusobacterium and Neisseriaceae were decreased, although none of

these differences was statistically significant. Future studies with more

participants and a greater range of arsenic exposure are needed to further

elucidate the effects of drinking water arsenic consumption on respiratory



DOI: 10.3390/ijerph110202299

PMCID: PMC3945600

PMID: 24566055  [PubMed - indexed for MEDLINE]



26. Eur J Clin Microbiol Infect Dis. 2015 Jul;34(7):1337-46. doi:

10.1007/s10096-015-2355-4. Epub 2015 Mar 12.


Study of the diversity and short-chain fatty acids production by the bacterial

community in overweight and obese Mexican children.


Murugesan S(1), Ulloa-Martínez M, Martínez-Rojano H, Galván-Rodríguez FM,

Miranda-Brito C, Romano MC, Piña-Escobedo A, Pizano-Zárate ML, Hoyo-Vadillo C,

García-Mena J.


Author information:

(1)Departamento de Genética y Biología Molecular, Cinvestav-IPN Unidad Zacatenco,

México, DF, 07360, Mexico.


Obesity and overweight are health problems of multifactorial etiology, which may

include changes in the microbiome. In Mexico, more than 30 % of the child

population between 5 and 11 years of age suffer from being overweight or are

obese, which makes it a public health issue in progress. The purpose of this work

was to measure the short-chain fatty acid concentration by high-performance

liquid chromatography (HPLC), and to characterize the bacterial diversity by ion

torrent semiconductor sequencing, of 16S rDNA libraries prepared from stools

collected from a sample of well-characterized Mexican children for normal weight,

overweight, and obese conditions by anthropometric and biochemical criteria. We

found that triglyceride levels are increased in overweight and obese children,

who presented altered propionic and butyric acid concentrations in feces. In

addition, although the colon microbiota did not show a clear bacterial dysbiosis

among the three conditions, the abundance of some particular bacteria was changed

with respect to normal controls. We conclude from our results that the imbalance

in the abundance of at least nine different bacteria as well as altered

short-chain fatty acid concentration in feces is associated to the overweight and

obese conditions of Mexican children.


DOI: 10.1007/s10096-015-2355-4

PMID: 25761741  [PubMed - indexed for MEDLINE]



27. Curr Microbiol. 2016 Mar;72(3):267-75. doi: 10.1007/s00284-015-0947-y. Epub 2015

Nov 28.


Comparative Analysis of Microbial Diversity in Termite Gut and Termite Nest Using

Ion Sequencing.


Manjula A(1), Pushpanathan M(2), Sathyavathi S(1), Gunasekaran P(1), Rajendhran



Author information:

(1)Department of Genetics, Centre for Excellence in Genomic Sciences, School of

Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021,

India. (2)Laboratory of Gene Regulation and Development, National Institute of

Child Health and Human Development, National Institutes of Health, Bethesda,

20892, MD, USA. (3)Department of Genetics, Centre for Excellence in Genomic

Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai,

Tamil Nadu, 625021, India.


Termite gut and termite nest possess complex microbial communities. However, only

limited information is available on the comparative investigation of termite gut-

and nest-associated microbial communities. In the present study, we examined and

compared the bacterial diversity of termite gut and their respective nest by

high-throughput sequencing of V3 hypervariable region of 16S rDNA. A total of 14

barcoded libraries were generated from seven termite gut samples and their

respective nest samples, and sequenced using Ion Torrent platform. The sequences

of each group were pooled, which yielded 170,644 and 132,000 reads from termite

gut and termite nest samples, respectively. Phylogenetic analysis revealed

significant differences in the bacterial diversity and community structure

between termite gut and termite nest samples. Phyla Verrucomicrobia and

Acidobacteria were observed only in termite gut, whereas Synergistetes and

Chlorobi were observed only in termite nest samples. These variations in

microbial structure and composition could be attributed with the differences in

physiological conditions prevailing in the termite gut (anoxic and alkaline) and

termite nest (oxic, slightly acidic and rich in organic matter) environment.

Overall, this study unmasked the complexity of bacterial population in the

respective niche. Interestingly, majority of the sequence reads could be

classified only up to the domain level indicating the presence of a huge number

of uncultivable or unidentified novel bacterial species in both termite gut and

nest samples. Whole metagenome sequencing and assessing the metabolic potential

of these samples will be useful for biotechnological applications.


DOI: 10.1007/s00284-015-0947-y

PMID: 26613615  [PubMed - in process]



28. PLoS One. 2016 Feb 26;11(2):e0150306. doi: 10.1371/journal.pone.0150306.

eCollection 2016.


Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development

of the Gut Microbial Community in Preterm Infants.


Zeber-Lubecka N(1), Kulecka M(1), Ambrozkiewicz F(1), Paziewska A(1), Lechowicz

M(2), Konopka E(3), Majewska U(2), Borszewska-Kornacka M(2), Mikula M(4),

Cukrowska B(3), Ostrowski J(1,)(4).


Author information:

(1)Department of Gastroenterology, Hepatology and Clinical Oncology, Medical

Center for Postgraduate Education, Warsaw, Poland. (2)Neonatal and Intensive Care

Department, Medical University of Warsaw, Warsaw, Poland. (3)Department of

Pathology, The Children's Memorial Health Institute, Warsaw, Poland.

(4)Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and

Institute of Oncology, Warsaw, Poland.


BACKGROUND: Recent advances in culture-independent approaches have enabled

insights into the diversity, complexity, and individual variability of gut

microbial communities.

OBJECTIVES: To examine the effect of oral administration of Saccharomyces (S.)

boulardii and mode of delivery on the intestinal microbial community in preterm


STUDY DESIGN: Stool samples were collected from preterm newborns randomly divided

into two groups: a probiotic-receiving group (n = 18) or a placebo group (n =

21). Samples were collected before probiotic intake (day 0), and after 2 and 6

weeks of supplementation. The composition of colonizing bacteria was assessed by

16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S

Metagenomics Kit and the Ion Torrent Personal Genome Machine platform.

RESULTS: A total of 11932257 reads were generated, and were clustered into 459,

187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks,

respectively. Of the 17 identified phyla, Firmicutes Actinobacteria,

Proteobacteria, and Bacteroidetes were universal. The microbial community

differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for

increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and

infants with a gestational age of 31 weeks or higher presented increased

bacterial diversity prior to S. boulardii administration. Firmicutes and

Proteobacteria remained stable during the observation period, whereas

Actinobacteria and Bacteroidetes increased in abundance, the latter particularly

more sharply in vaginally delivered infants.

CONCLUSION: While the mode of delivery may influence the development of a

microbial community, this study had not enough power to detect statistical

differences between cohorts supplemented with probiotics, and in a consequence,

to speculate on S. boulardii effect on gut microbiome composition in preterm



DOI: 10.1371/journal.pone.0150306

PMCID: PMC4769247

PMID: 26918330  [PubMed - indexed for MEDLINE]