scholarly journals Humans differ in their personal microbial cloud

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1258 ◽  
Author(s):  
James F. Meadow ◽  
Adam E. Altrichter ◽  
Ashley C. Bateman ◽  
Jason Stenson ◽  
GZ Brown ◽  
...  
Keyword(s):  
16S Rrna ◽  
Indoor Air ◽  
Direct Contact ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Climate Chamber ◽  
Single Person ◽  
First Time

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

scholarly journals Status of the Archaeal and Bacterial Census: an Update

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Patrick D. Schloss ◽  
Rene A. Girard ◽  
Thomas Martin ◽  
Joshua Edwards ◽  
J. Cameron Thrash
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
New Technologies ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Short Read ◽  
Sequencing Technologies

ABSTRACT A census is typically carried out for people across a range of geographical levels; however, microbial ecologists have implemented a molecular census of bacteria and archaea by sequencing their 16S rRNA genes. We assessed how well the census of full-length 16S rRNA gene sequences is proceeding in the context of recent advances in high-throughput sequencing technologies because full-length sequences are typically used as references for classification of the short sequences generated by newer technologies. Among the 1,411,234 and 53,546 full-length bacterial and archaeal sequences, 94.5% and 95.1% of the bacterial and archaeal sequences, respectively, belonged to operational taxonomic units (OTUs) that have been observed more than once. Although these metrics suggest that the census is approaching completion, 29.2% of the bacterial and 38.5% of the archaeal OTUs have been observed more than once. Thus, there is still considerable diversity to be explored. Unfortunately, the rate of new full-length sequences has been declining, and new sequences are primarily being deposited by a small number of studies. Furthermore, sequences from soil and aquatic environments, which are known to be rich in bacterial diversity, represent only 7.8 and 16.5% of the census, while sequences associated with host-associated environments represent 55.0% of the census. Continued use of traditional approaches and new technologies such as single-cell genomics and short-read assembly are likely to improve our ability to sample rare OTUs if it is possible to overcome this sampling bias. The success of ongoing efforts to use short-read sequencing to characterize archaeal and bacterial communities requires that researchers strive to expand the depth and breadth of this census. IMPORTANCE The biodiversity contained within the bacterial and archaeal domains dwarfs that of the eukaryotes, and the services these organisms provide to the biosphere are critical. Surprisingly, we have done a relatively poor job of formally tracking the quality of the biodiversity as represented in full-length 16S rRNA genes. By understanding how this census is proceeding, it is possible to suggest the best allocation of resources for advancing the census. We found that the ongoing effort has done an excellent job of sampling the most abundant organisms but struggles to sample the rarer organisms. Through the use of new sequencing technologies, we should be able to obtain full-length sequences from these rare organisms. Furthermore, we suggest that by allocating more resources to sampling environments known to have the greatest biodiversity, we will be able to make significant advances in our characterization of archaeal and bacterial diversity.

scholarly journals Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Ma ◽  
Geng Wu ◽  
Jian Yang ◽  
Liuqin Huang ◽  
Dorji Phurbu ◽  
...  
Keyword(s):  
Community Structure ◽  
Hydrogen Production ◽  
16S Rrna ◽  
High Throughput Sequencing ◽  
Hot Springs ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Tibetan Plateau

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

scholarly journals Characterization of Bioaerosols from Dairy Barns: Reconstructing the Puzzle of Occupational Respiratory Diseases by Using Molecular Approaches

2012 ◽  
Vol 78 (9) ◽  
pp. 3242-3248 ◽  
Author(s):  
Pascale Blais Lecours ◽  
Marc Veillette ◽  
David Marsolais ◽  
Caroline Duchaine
Keyword(s):  
16S Rrna ◽  
Respiratory Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Exact Nature ◽  
Continuous Exposure ◽  
Content Type ◽  
Humoral Immune ◽  
Molecular Approaches ◽  
First Time

ABSTRACTTo understand the etiology of exposure-related diseases and to establish standards for reducing the risks associated with working in contaminated environments, the exact nature of the bioaerosol components must be defined. Molecular biology tools were used to evaluate airborne bacterial and, for the first time, archaeal content of dairy barns. Three air samplers were tested in each of the 13 barns sampled. Up to 106archaeal and 108bacterial 16S rRNA genes per m3of air were detected. Archaeal methanogens, mainlyMethanobrevibacterspecies, were represented.Saccharopolyspora rectivirgula, the causative agent of farmer's lung, was quantified to up to 10716S rRNA genes per m3of air. In addition, a wide variety of bacterial agents were present in our air samples within the high airborne bioaerosol concentration range. Despite recommendations regarding hay preservation and baling conditions, farmers still develop anS. rectivirgula-specific humoral immune response, suggesting intense and continuous exposure. Our results demonstrate the complexity of bioaerosol components in dairy barns which could play a role in occupational respiratory diseases.

scholarly journals Effects of Gasterophilus pecorum infestation on the intestinal microbiota of the rewilded Przewalski’s horses in China

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251512
Author(s):  
Dini Hu ◽  
Yuzhu Chao ◽  
Boru Zhang ◽  
Chen Wang ◽  
Yingjie Qi ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Nature Reserve ◽  
Sequence Data ◽  
Parasitic Infection ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bioinformatics Analyses ◽  
Gasterophilus Pecorum ◽  
First Time

Horse botflies have been a threat to the Przewalski’s horses in the Kalamaili Nature Reserve in Xinjiang of China since their reintroduction to the original range. As larvae of these parasites could infest the intestine of a horse for months, they could interact with and alter the structure and composition of its intestinal microbiota, affecting adversely its health. Nonetheless, there are no such studies on the rewilded Przewalski’s horses yet. For the first time, this study characterizes the composition of the intestinal microbiota of 7 rewilded Przewalski’s horses infected severely by Gasterophilus pecorum following and prior to their anthelmintic treatment. Bioinformatics analyses of the sequence data obtained by amplicon high throughput sequencing of bacterial 16S rRNA genes showed that G. pecorum infestation significantly increased the richness of the intestinal microbial community but not its diversity. Firmicutes and Bacteroidetes were found the dominant phyla as in other animals, and the parasitic infestation decreased the F/B ratio largely by over 50%. Large reduction in relative abundances of the two genera Streptococcus and Lactobacillus observed with G. pecorum infestation suggested possible changes in colic and digestion related conditions of the infected horses. Variations on the relative abundance of the genus groups known to be pathogenic or symbiotic showed that adverse impact of the G. pecorum infestation could be associated with reduction of the symbiotic genera Lactobacillus and Bifidobacterium that are probiotics and able to promote immunity against parasitic infection.

scholarly journals The relationship between benthic nutrient fluxes and bacterial community in Aquaculture tail-water treatment systems

2021 ◽  
Author(s):  
Regan Nicholaus ◽  
Betina Lukwambe ◽  
Wen Yang ◽  
Zhongming Zheng
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Constructed Wetland ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Fluxes ◽  
Benthic Nutrient Fluxes ◽  
Tail Water

Constructed-wetlands, Biofilms, and sedimentation are potential aquaculture tail-water treatments however their roles on the distribution of benthic microbial community and the way they affect the interaction between microbial community and inorganic nutrient fluxes have not been fully explored. This study applied 16S rRNA high-throughput sequencing technology to investigate the microbial community distribution and their link with nutrient fluxes in an aquaculture tail- water bioremediation system . Results showed that bacterial community compositions were significantly different in constructed-wetland and biofilm treatments (p<0.05) relative to sedimentation. The composition of the 16S rRNA genes among all the treatments was enriched with Proteobacteria, Bacteroidetes, Firmicutes, and Flavobacteria . NMDS analysis showed that the bacterial composition in constructed-wetland and biofilm samples clustered separately compared to those in sedimentation. The Functional-Annotation-of-Prokaryotic-Taxa analysis indicated that the proportions of sediment-microbial-functional groups (aerobic-chemoheterophy, chemoheterotrophy, and nitrate-ammonification combined) in the constructed-wetland treatment were 47%, 32% in biofilm and 13% in sedimentation system. Benthic-nutrient fluxes for phosphate, ammonium, nitrite, nitrate and sediment oxygen consumption differed markedly among the treatments ( p<0.05 ). Canonical correspondence analysis indicated constructed-wetland had the strongest association between biogeochemical contents and the bacterial community relative to other treatments. This study suggests that the microbial community distributions and their interactions nutrient fluxes were most improved in the constructed-wetland followed by the area under biofilm and sedimentation treatment.

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