scholarly journals Microbiome analyses and presence of cable bacteria in the burrow sediment of Upogebia pugettensis

2020 ◽  
Vol 648 ◽  
pp. 79-94
Author(s):  
C Li ◽  
CE Reimers ◽  
JW Chapman
Keyword(s):  
Bacterial Community ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Estuarine Sediments ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Northeastern Pacific ◽  
Upogebia Pugettensis ◽  
Rrna Gene Sequencing ◽  
Catalyzed Reporter Deposition

We utilized methods of sediment cultivation, catalyzed reporter deposition-fluorescence in situ hybridization, scanning electron microscopy, and 16s rRNA gene sequencing to investigate the presence of novel filamentous cable bacteria (CB) in estuarine sediments bioturbated by the mud shrimp Upogebia pugettensis Dana and also to test for trophic connections between the shrimp, a commensal bivalve (Neaeromya rugifera), and the sediment. Agglutinated sediments from the linings of shrimp burrows exhibited higher abundances of CB compared to surrounding suboxic and anoxic sediments. Furthermore, CB abundance and activity increased in these sediments when they were incubated under oxygenated seawater. Through core microbiome analysis, we found that the microbiomes of the shrimp and bivalve shared 181 taxa with the sediment bacterial community, and that these shared taxa represented 17.9% of all reads. Therefore, bacterial biomass in the burrow sediment lining is likely a major food source for both the shrimp and the bivalve. The biogeochemical conditions created by shrimp burrows and other irrigators may help promote the growth of CB and select for other dominant members of the bacterial community, particularly a variety of members of the Proteobacteria. These associations give new understanding to the ecology of a burrowing crustacean that is common, but in decline, throughout intertidal mudflats of Northeastern Pacific estuaries.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

scholarly journals The international sinonasal microbiome study (ISMS): a multi-centre, multi-national collaboration characterising the microbial ecology of the sinonasal cavity

2019 ◽  
Author(s):  
Sathish Paramasivan ◽  
Ahmed Bassiouni ◽  
Arron Shiffer ◽  
Matthew R Dillon ◽  
Emily K Cope ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Relative Abundance ◽  
Current Knowledge ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Knowledge Based ◽  
Geographical Variations ◽  
Health And Disease ◽  
Rrna Gene Sequencing

ABSTRACTThe sinonasal microbiome remains poorly defined, with our current knowledge based on a few cohort studies whose findings are inconsistent. Furthermore, the variability of the sinus microbiome across geographical divides remains unexplored. We characterise the sinonasal microbiome and its geographical variations in both health and disease using 16S rRNA gene sequencing of 410 individuals from across the world. Although the sinus microbial ecology is highly variable between individuals, we identify a core microbiome comprised of Corynebacterium, Staphylococcus, Streptococcus, Haemophilus, and Moraxella species in both healthy and chronic rhinosinusitis (CRS) cohorts. Corynebacterium (mean relative abundance = 44.02%) and Staphylococcus (mean relative abundance = 27.34%) appear particularly dominant in the majority of patients sampled. There was a significant variation in microbial diversity between countries (p = 0.001). Amongst patients suffering from CRS with nasal polyps, a significant depletion of Corynebacterium (40.29% vs 50.43%; p = 0.02) and over-representation of Streptococcus (7.21% vs 2.73%; p = 0.032) was identified. The delineation of the sinonasal microbiome and standardised methodology described within our study will enable further characterisation and translational application of the sinus microbiota.

scholarly journals Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

2016 ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Atsushi Tanaka ◽  
Ayato Kohzu ◽  
Hideo Oyagi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Layer ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Freshwater Lakes ◽  
Ecological Importance ◽  
Rrna Gene Sequencing ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

ABSTRACTFreshwater bacterioplankton in the oxygenated hypolimnion are reportedly dominated by specific members that are distinct from those in the epilimnion. However, no consensus exists regarding the ubiquity and abundance of these bacterioplankton, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that many predominant lineages in the hypolimnion were shared by several lakes and consisted of members occurring in the entire water layer and members specific to the hypolimnion. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed that representative hypolimnion-specific lineages, CL500–11 (Chloroflexi), CL500–3, CL500–37, CL500–15 (Planctomycetes), and the MGI group (Thaumarchaeota), together accounted for 1.5–32.9% of all bacterioplankton in the hypolimnion of the lakes. Furthermore, an analysis of micro-diversification based on single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of hypolimnion-specific ecotypes among the lineages occurring in the entire water layer (e.g., acI and Limnohabitans). Collectively, these results demonstrate the uniqueness, ubiquity, and quantitative significance of bacterioplankton in the oxygenated hypolimnion, motivating future studies to focus on their eco-physiological characteristics.

scholarly journals ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Isabel Abellan-Schneyder ◽  
Andrea Janina Schusser ◽  
Klaus Neuhaus
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Limiting Factor ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Dna Amounts

Abstract Background One limiting factor of short amplicon 16S rRNA gene sequencing approaches is the use of low DNA amounts in the amplicon generation step. Especially for low-biomass samples, insufficient or even commonly undetectable DNA amounts can limit or prohibit further analysis in standard protocols. Results Using a newly established protocol, very low DNA input amounts were found sufficient for reliable detection of bacteria using 16S rRNA gene sequencing compared to standard protocols. The improved protocol includes an optimized amplification strategy by using a digital droplet PCR. We demonstrate how PCR products are generated even when using very low concentrated DNA, unable to be detected by using a Qubit. Importantly, the use of different 16S rRNA gene primers had a greater effect on the resulting taxonomical profiles compared to using high or very low initial DNA amounts. Conclusion Our improved protocol takes advantage of ddPCR and allows faithful amplification of very low amounts of template. With this, samples of low bacterial biomass become comparable to those with high amounts of bacteria, since the first and most biasing steps are the same. Besides, it is imperative to state DNA concentrations and volumes used and to include negative controls indicating possible shifts in taxonomical profiles. Despite this, results produced by using different primer pairs cannot be easily compared.

scholarly journals Distinctly different bacterial communities in surface and oxygen minimum layers in the Arabian Sea

2016 ◽  
Author(s):  
Mandar Bandekar ◽  
Nagappa Ramaiah ◽  
Anand Jain ◽  
Ram Murti Meena
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Arabian Sea ◽  
16S Rrna Gene Sequencing ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Northeast Monsoon ◽  
Rrna Gene Sequencing ◽  
Oxygen Minimum

Abstract. Contributions of microbial communities to biogeochemical processes in oxygen minimum oceanic zones are being realized through the applications of molecular techniques. To understand seasonal and depth-wise variations in bacterial community structure (BCS) in the Arabian Sea oxygen minimum region, extensive sampling and molecular analyses were carried out. 16S rRNA gene sequencing was done to profile the BCS from five depths, surface (5 m), deep chorophyll maximum (43–50 m, DCM), 250 m, 500 m and 1000 m during Spring intermonsoon (SIM), Fall intermonsoon (FIM), and Northeast monsoon (NEM) seasons. Sequencing of 743 chimera-free clones revealed a clear vertical partitioning of BCS between the surface (surface + DCM) and OMZ (250 + 500 + 1000 m) layers. There was no distinct seasonal difference in the BCS. Most 16S rRNA gene sequences were affiliated to Gammaproteobacteria (39.31 %), Alphaproteobacteria (23.56 %) and Cyanobacteria (20.2 %). Higher diversity and OTUs in OMZ predominantly consisting of Alteromonodales, Sphinogomonadales, Rhodobacterales, Burkholderales, and Acidimicrobiales we observed might be due to their microaerophilic metabolism, ability to degrade recalcitrant substrates and assimilate sinking particulate matter. Further hitherto undescribed diversity both in surface and OMZ layers was evidenced. Implicit role of extant bacterial community in denitrification and anammox and in sulphur oxidation is highlighted.

scholarly journals Sex Results in Divergence in Gut Bacterial Community between Female and Male Pardosa astrigera (Araneae: Lycosidae)

2021 ◽  
Author(s):  
Ying Gao ◽  
Pengfeng Wu ◽  
Shuyan Cui ◽  
Abid Ali ◽  
Guo Zheng
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Factors Affecting ◽  
Β Diversity ◽  
Pardosa Astrigera ◽  
Rrna Gene Sequencing ◽  
Agro Forestry

Sex is one of the important factors affecting gut microbiota. As key predators in agro-forestry ecosystem, many spider species show dramatically different activity habits and nutritional requirements between female and male. However, how sex affects gut microbiota of spiders is still unclear. Therefore, in this study, the compositions and diversities of gut bacteria, based on bacterial 16S rRNA gene sequencing, were compared between female and male Pardosa astrigera. We found that bacterial richness indices (P < 0.05) in female were significantly lower than male, meanwhile, β-diversity showed significantly different between female and male (P < 0.05). The relative abundance of Actinobacteriota and Rhodococcus (belongs to Actinobacteria) were significantly higher in female than male (P < 0.05). Whereas, the relative abundance of Firmicutes and Acinetobacter (belongs to Proteobacteria), Ruminococcus and Fusicatenibacter (all belong to Firmicutes), were significantly higher in male than female (P < 0.05). The results of PICRUSt2 showed that amino acid and lipid metabolisms were significantly higher in female than male (P < 0.05), whereas glycan biosynthesis and metabolism was significantly higher in male than female (P < 0.05). Our results imply that sexual variation is a crucial factor in shaping gut bacterial community in P. astrigera. Male P. astrigera dispersed more widely than the female hence the male had a higher bacterial diversity. While the distinct differences of bacterial composition mainly due to their different nutritional and energy requirements.

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