Raman‐FISH: combining stable‐isotope Raman spectroscopy and fluorescence <i>in situ</i> hybridization for the single cell analysis of identity and function

Huang, Wei E.; Stoecker, Kilian; Griffiths, Robert I.; Newbold, Lindsay K.; Daims, Holger; Whiteley, Andrew S.; Wagner, Michael

doi:10.1111/j.1462-2920.2007.01352.x

Cited by 297 publications

(301 citation statements)

References 61 publications

(67 reference statements)

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“…However, to date, Raman microscopy has often been used together with FISH (Raman-FISH) to differentiate microbial populations such as Bacteria and Archaea (Huang et al, 2007). On the contrary, SR-FTIR does not require cell labeling.…”

Section: Discussionmentioning

confidence: 99%

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

et al. 2012

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Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.

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Section: Discussionmentioning

confidence: 99%

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

et al. 2012

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“…Methods for isolating cells and characterizing their genomes are expected to become increasingly sophisticated and high throughput (Lasken, 2007;Marcy et al, 2007a), especially methods that target organisms associated with the 'rare biosphere' (Sogin et al, 2006) and techniques specifically linked to the incorporation of labelled substrates (Huang et al, 2007). As a result, the use of MDA to obtain genomic DNA from single cells is anticipated to play a central and increasing role in accessing genetic and ecological information associated with uncultivated microorganisms.…”

Section: Use Of Mda In Microbial Ecologymentioning

confidence: 99%

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

2008

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Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

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“…Fluorescence in situ hybridization (FISH) was used to identify target populations for Raman microspectroscopic analysis, which utilizes the principle of Raman scattering to chemically fingerprint individual microbial cells (Huang et al, 2007). The probes used in the present study were Bac-0303 5 0 -CCA ATG TGG GGG ACC TT-3 0 (Manz et al, 1996) and Erec-0482 5 0 -CGC GGC ATT GCT CGT TCA-3 0 (Franks et al, 1998) (Thermo Fisher Scientific, Vienna, Austria).…”

Section: Confocal Raman Microspectroscopymentioning

confidence: 99%

High-fat diet alters gut microbiota physiology in mice

Daniel¹,

Gholami²,

Berry³

et al. 2013

The ISME Journal

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588

386

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The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by highcalorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared-(FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via highresolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.

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Raman‐FISH: combining stable‐isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function

Cited by 297 publications

References 61 publications

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

High-fat diet alters gut microbiota physiology in mice

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