Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Abstract Background Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

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Characterization of the salivary microbiome in people with obesity

PeerJ ◽

10.7717/peerj.4458 ◽

2018 ◽

Vol 6 ◽

pp. e4458 ◽

Cited By ~ 25

Author(s):

Yujia Wu ◽

Xiaopei Chi ◽

Qian Zhang ◽

Feng Chen ◽

Xuliang Deng

Keyword(s):

High Throughput Sequencing ◽

Periodontal Diseases ◽

Illumina Miseq ◽

Normal Weight ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Diseases ◽

And Function ◽

Healthy Participants

Background The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs. Methods We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases. Results The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls. Discussion Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases.

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Bacterial Diversity and Community in Regional Water Microbiota between Different Towns in World’s Longevity Township Jiaoling, China

Diversity ◽

10.3390/d13080361 ◽

2021 ◽

Vol 13 (8) ◽

pp. 361

Author(s):

Lei Wu ◽

Xinqiang Xie ◽

Jumei Zhang ◽

Yu Ding ◽

Qingping Wu

Keyword(s):

16S Rrna ◽

High Throughput Sequencing ◽

The Other ◽

Rrna Gene ◽

Metabolic Characteristics ◽

Kegg Pathways ◽

Healthy Longevity ◽

And Function ◽

Regional Water

Healthy longevity is associated with many factors, however, the potential correlation between longevity and microbiota remains elusive. To address this, we explored environmental microbiota from one of the world’s longevity townships in China. We used 16S rRNA gene high-throughput sequencing to analyze the composition and function of water microbiota. The composition and diversity of water microbiota significantly differed between the towns. Lactobacillus, Streptococcus, Bacteroides, Faecalibacterium, and Stenotrophomonas were only dominant in Xinpu, a town with an exceptionally high centenarian population. Several biomarkers were identified, including Flavobacterium, Acinetobacter, Paracoccus, Lactobacillales, Psychrobacter, Bacteroides, Ruminococcaceae, and Faecalibacterium, and these shown to be responsible for the significant differences between towns. The main species contributing to the differences between towns were Cyanobacteria, Cupriavidus and Ralstonia. Based on KEGG pathways showed that the predicted metabolic characteristics of the water microbiota in Xinpu towns were significantly different to those of the other towns. The results revealed significant differences in the composition and diversity of water microbiota in the longevity township. These findings provide a foundation for further research on the role of water microbiota in healthy longevity.

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Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform

mSystems ◽

10.1128/msystems.00029-19 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 17

Author(s):

Johanna B. Holm ◽

Michael S. Humphrys ◽

Courtney K. Robinson ◽

Matthew L. Settles ◽

Sandra Ott ◽

...

Keyword(s):

High Throughput Sequencing ◽

Sequence Data ◽

Microbial Community Composition ◽

Pcr Amplification ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Illumina Hiseq ◽

Illumina Miseq Platform ◽

Miseq Platform

ABSTRACT Amplification, sequencing, and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300-bp paired-end reads of higher quality than those produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-step PCR amplification protocol is also described that allows for targeting of different amplicon regions, and enhances amplification success from samples with low bacterial bioburden. IMPORTANCE Amplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high-throughput sequencing have made it a widely adopted approach, especially for projects that necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per-sample cost relative to those of the Illumina MiSeq platform without sacrificing amplicon length. To make this method more flexible for various amplicon-targeted regions as well as improve amplification from low-biomass samples, we also present and validate a 2-step PCR library preparation method.

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Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

Applied and Environmental Microbiology ◽

10.1128/aem.00520-16 ◽

2016 ◽

Vol 82 (12) ◽

pp. 3525-3536 ◽

Cited By ~ 9

Author(s):

Nikea Ulrich ◽

Abigail Rosenberger ◽

Colin Brislawn ◽

Justin Wright ◽

Collin Kessler ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Storm Event ◽

Rrna Gene ◽

Content Type

ABSTRACTBacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in whichBetaproteobacteriaandGammaproteobacteriadecreased in 16S rRNA gene relative abundance, while the relative abundance of members of theFirmicutesincreased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains ofLegionella,Campylobacter,Arcobacter, andHelicobacter, as well as bacteria of fecal origin (e.g.,Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.IMPORTANCEIn order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.

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Marine cyanolichens from different littoral zones are associated with distinct bacterial communities

PeerJ ◽

10.7717/peerj.5208 ◽

2018 ◽

Vol 6 ◽

pp. e5208 ◽

Cited By ~ 6

Author(s):

Nyree J. West ◽

Delphine Parrot ◽

Claire Fayet ◽

Martin Grube ◽

Sophie Tomasi ◽

...

Keyword(s):

Bacterial Communities ◽

Littoral Zone ◽

Resistant Bacteria ◽

Rrna Gene ◽

Moderately Thermophilic ◽

Culture Independent ◽

Radiation Resistant ◽

Bacteroidetes Phylum ◽

And Function ◽

The Impact

The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen speciesLichina pygmaeaandLichina confinis, and the maritime chlorolichen speciesXanthoria aureolawhich occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. TheL. confinisandL. pygmaeacommunities were significantly different from those of the maritimeXanthoria aureolalichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notablySphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the twoLichinaspecies were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes generaRubricoccus,TunicatimonasandLewinella, suggesting an important role of these species in the marineLichinalichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.

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Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

10.1101/2020.03.19.998526 ◽

2020 ◽

Author(s):

Alyssa Kent ◽

Albert Vill ◽

Qiaojuan Shi ◽

Michael J. Satlin ◽

Ilana Lauren Brito

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Healthy Individuals ◽

Hematopoietic Stem ◽

Culture Independent ◽

Neutropenic Patients ◽

Mobile Ar ◽

And Function

AbstractThe gut microbiome harbors a ‘silent reservoir’ of antibiotic resistance (AR) genes that is thought to contribute to the emergence of multidrug-resistant pathogens through the process of horizontal gene transfer (HGT). To counteract the spread of AR genes, it is paramount to know which organisms harbor mobile AR genes and with which organisms they engage in HGT. Despite methods to characterize the bulk presence1, abundance2 and function3 of AR genes in the gut, technological limitations of short-read sequencing have precluded linking bacterial taxa to specific mobile genetic elements (MGEs) and their concomitant AR genes. Here, we apply and evaluate a high-throughput, culture-independent method for surveilling the bacterial carriage of MGEs, based on bacterial Hi-C protocols. We compare two healthy individuals with a cohort of seven neutropenic patients undergoing hematopoietic stem cell transplantation, who receive multiple courses of antibiotics throughout their prolonged hospitalizations, and are thus acutely vulnerable to the threat of multidrug-resistant infections4. We find that the networks of HGT are surprisingly distinct between individuals, yet AR and mobile genes are more dispersed across taxa within the neutropenic patients than the healthy subjects. Our data further suggest that HGT is occurring throughout the course of treatment in the microbiomes of neutropenic patients and within the guts of healthy individuals over a similar timeframe. Whereas most efforts to understand the spread of AR genes have focused on pathogenic species, our findings shed light on the role of the human gut microbiome in this process.

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Effect of mare’s milk prebiotic supplementation on the gut microbiome and the immune system following antibiotic therapy

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d211110 ◽

2020 ◽

Vol 21 (11) ◽

Author(s):

Madiyar Nurgaziyev ◽

YERMEK AITENOV ◽

ZHANAGUL KHASSENBEKOVA ◽

SANIYA AKPANOVA ◽

KAIRAT RYSBEKOV ◽

...

Keyword(s):

Immune System ◽

Antibiotic Therapy ◽

Antibiotic Treatment ◽

Gut Microbiome ◽

Taxonomic Composition ◽

Rrna Gene ◽

Total Dna ◽

And Function ◽

V3 Region

Abstract. Nurgaziyev M, Atenov Y, Khassenbekova Z, Akpanova S, Rysbekov K, Kozhakhmetov S, Nurgozhina A, Sergazy S, Chulenbayeva L, Ospanova Z, Tuyakova A, Mukhambetganov N, Sattybayeva R, Urazova S, Galymgozhina N, Zhumadilova A, Gulyaev A, Kushugulova A. 2020. Effect of mare’s milk prebiotic supplementation on the gut microbiome and the immune system following antibiotic therapy. Biodiversitas 21: 5065-5071. Antibiotic treatment can severely affect the gut microbiome for short-term and long-term consequences. Probiotic and prebiotic supplements are widely prescribed to modulate the composition and function of the human gut microbiome. The current study aims to determine the impacts of mare’s milk prebiotics on the diversity of gut bacterial communities and the local immune system when administered during and after a course of antibiotic therapy. Six children aged 4 to 5 years diagnosed with bilateral bronchopneumonia were prescribed cephalosporin (cefuroxime) antibiotics. During the 60 days of the study, three children consumed mare’s milk prebiotics, while the other three did not. Fecal samples were collected daily during antibiotic therapy and every five days after the last day of antibiotic treatment. Total DNA was isolated, and the taxonomic composition of the gut microbiome was analyzed by sequencing the 16S rRNA gene (V1-V3 region). The MULTIPLEX MAP platform was used to evaluate the local immune status. The relative abundance of 11 genera was reduced and did not recover until the last day of the study. The abundance of Bacteroides was not significantly altered in either group. Christensenella, Rothia, Abiotrophia, Acinetobacter, Anaerotruncus, Holdemania, and Turicibacter numbers were significantly increased on day five and remained at the same level during the study period. Cephalosporin administration also reduced the levels of pro-inflammatory and anti-inflammatory cytokines/chemokines (MIP1α, TNFα, GMCSF, GCSF, sCD40L, FGF2, TGFα, IL1α, and IP10).

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Ultra-high throughput multiplexing and sequencing of >500 bp amplicon regions on the Illumina HiSeq 2500 platform

10.1101/417618 ◽

2018 ◽

Cited By ~ 3

Author(s):

Johanna B. Holm ◽

Michael S. Humphrys ◽

Courtney K. Robinson ◽

Matthew L. Settles ◽

Sandra Ott ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Sequence Data ◽

Microbial Community Composition ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Illumina Hiseq ◽

Illumina Miseq Platform ◽

Miseq Platform

AbstractAmplification, sequencing and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300 bp paired-end reads of higher quality than produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-Step PCR amplification protocol is also described that allows for targeting of different amplicon regions, thus improving amplification success from low bacterial bioburden samples.ImportanceAmplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high throughput sequencing have made it a widely-adopted approach, especially for projects which necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per sample cost relative to the Illumina MiSeq platform, without sacrificing amplicon length. To make this method more flexible to various amplicon targeted regions as well as improve amplification from low biomass samples, we also present and validate a 2-Step PCR library preparation method.

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Impact of Host Genetics on Caecal Microbiota Composition and on Salmonella Carriage in Chicken

10.21203/rs.3.rs-76645/v1 ◽

2020 ◽

Author(s):

Anaïs Cazals ◽

Jordi ESTELLÉ ◽

Nicolas BRUNEAU ◽

Jean-Luc COVILLE ◽

Pierrette MENANTEAU ◽

...

Keyword(s):

High Throughput Sequencing ◽

Genetic Selection ◽

Digital Pcr ◽

Taxonomic Composition ◽

Rrna Gene ◽

Microbiota Composition ◽

Experimental Conditions ◽

Host Genetics ◽

Abundant Otus ◽

Caecal Microbiota

Abstract Background Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication through the consumption of contaminated poultry products. Genetic selection of animals more resistant to Salmonella carriage and the modulation of gut microbiota are two promising ways of decreasing individual Salmonella carriage. This study aims to identify the main genetic and microbial factors controlling the individual levels of Salmonella carriage in chickens (Gallus gallus) in controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines, N and 61, were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce the recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition through a 16S rRNA gene high-throughput sequencing approach. Results Results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Out of 617 Operational Taxonomic Units (OTUs), over 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between high and low Salmonella carriers, with 39 differentially abundant OTUs. Finally, via metagenome functional prediction based on 16S data, we identified several metabolic pathways potentially associated to microbiota taxonomic differences (e.g. butyrate metabolism) between high and low carriers. Conclusions Overall, this study demonstrates that the caecal microbiota composition of the N and 61 lines is influenced by the host genetics, which could be one of the reasons why these lines differ for their Salmonella carriage in experimental infection conditions.

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Diversity, spatial distribution and activity of fungi in freshwater ecosystems

PeerJ ◽

10.7717/peerj.6247 ◽

2019 ◽

Vol 7 ◽

pp. e6247 ◽

Cited By ~ 8

Author(s):

Cécile Lepère ◽

Isabelle Domaizon ◽

Jean-Francois Humbert ◽

Ludwig Jardillier ◽

Mylène Hugoni ◽

...

Keyword(s):

18S Rrna ◽

High Throughput Sequencing ◽

Taxonomic Composition ◽

Freshwater Ecosystems ◽

Rrna Genes ◽

Active Fraction ◽

Catchment Areas ◽

Freshwater Habitats ◽

Taxonomic Affiliation ◽

18S Rrna Genes

High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.

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