RESEARCH PAPER Fast discrimination of bacteria using a filter paper–based SERS platform and PLS-DA with uncertainty estimation Javier E. L. Villa 1 & Nataly Ruiz Quiñones 2,3 & Fabiana Fantinatti-Garboggini 2 & Ronei J. Poppi 1 Received: 30 August 2018 /Revised: 5 November 2018 /Accepted: 7 November 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Rapid and reliable identification of bacteria is an important issue in food, medical, forensic, and environmental sciences; however, conventional procedures are time-consuming and often require extensive financial and human resources. Herein, we present a label-free method for bacterial discrimination using surface-enhanced Raman spectroscopy (SERS) and partial least squares discriminant analysis (PLS-DA). Filter paper decorated with gold nanoparticles was fabricated by the dip-coating method and it was utilized as a flexible and highly efficient SERS substrate. Suspensions of bacterial samples from three genera and six species were directly deposited on the filter paper–based SERS substrates before measurements. PLS-DA was successfully employed as a multivariate supervised model to classify and identify bacteria with efficiency, sensitivity, and specificity rates of 100% for all test samples. Variable importance in projection was associated with the presence/absence of some purine metabolites, whereas confidence intervals for each sample in the PLS-DA model were calculated using a resampling bootstrap procedure. Additionally, a potential new species of bacteria was analyzed by the proposed method and the result was in agreement with that obtained via 16S rRNA gene sequence analysis, thereby indicating that the SERS/PLS-DA approach has the potential to be a valuable tool for the discovery of novel bacteria. Keywords Surface-enhanced Raman spectroscopy . Gold nanoparticles . Chemometrics, partial least squares discriminant analysis . Reliability estimation . 16S rRNA gene sequence analysis Introduction Reliable and cost-effective discrimination of bacteria is an important issue in many fields such as human health care, food safety, forensic, and environmental sciences. Accordingly, several methods primarily based on plating and culturing be- fore physiological, biochemical, and genomic analysis have been routinely applied in microbiology. In particular, genetic analysis by the detection of the 16S rRNA gene provides an accurate way, not only to classify and identify bacteria but also for discovering novel bacterial species (when combined with phenotypic and chemotaxonomic data) [1, 2]. However, it can be tedious and complex and requires significant time, sophis- ticated instrumentation, and extensive human resources. Alternatively, vibrational (Raman or infrared) spectroscopy– based methods can provide a rapid way to discriminate bacteria because they allow obtaining structural and chemical informa- tion after minimal sample preparation [3, 4]. Despite its versa- tility and reduced susceptibility to contamination, these tech- niques also present some drawbacks which should be taken into consideration. For example, mid- and near-infrared spectrosco- py are limited by the presence of water usually found in bio- logical samples, resulting in significant interference signals that make spectral interpretation difficult. In contrast, the use of Raman spectroscopy guarantees minimal interference in aque- ous media because of the weak Raman activity of water. Nevertheless, the Raman analysis often requires large exposure times, owing to the inefficient inelastic scattering, and might Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00216-018-1485-9) contains supplementary material, which is available to authorized users. * Ronei J. Poppi ronei@iqm.unicamp.br 1 Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP 13081-970, Brazil 2 Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), University of Campinas (UNICAMP), Paulinia, SP 13148-218, Brazil 3 Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil Analytical and Bioanalytical Chemistry https://doi.org/10.1007/s00216-018-1485-9