The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach

Abstract

Microbial communities are ubiquitous in both natural and artificial environments. However, microbial diversity is usually reduced under strong selection pressures, such as those present in habitats rich in recalcitrant or toxic compounds displaying antimicrobial properties. Caffeine is a natural alkaloid present in coffee, tea and soft drinks with well-known antibacterial properties. Here we present the first systematic analysis of coffee machine-associated bacteria. We sampled the coffee waste reservoir of ten different Nespresso machines and conducted a dynamic monitoring of the colonization process in a new machine. Our results reveal the existence of a varied bacterial community in all the machines sampled, and a rapid colonisation process of the coffee leach. The community developed from a pioneering pool of enterobacteria and other opportunistic taxa to a mature but still highly variable microbiome rich in coffee-adapted bacteria. The bacterial communities described here, for the first time, are potential drivers of biotechnologically relevant processes including decaffeination and bioremediation.

Figure 1

(A) Schematic representation of a Nespresso machine (1) including a capsule (3) container (2), cup tray (4) and a drip tray (5), which was sampled in this work. (B) Bacterial profile of the nine Nespresso machines sampled according to 16S rRNA gene sequencing. Samples numbered in accordance to Table 1.

Figure 2. Bacterial colonisation in a brand new Nespresso Krups Inissia machine.

(A) Bacterial profile in the drip tray during the two months of operation according to 16S rRNA gene monitoring. (B) Ecological succession of the main taxa during the experiment, represented as the variation of their relative frequencies.

Figure 3. Correlations among the bacterial genera detected in this work.

Distances correspond to the linear statistical correlation. Sizes of the spheres are proportional to the relative abundances in logarithmic scale. Highly correlated genera are shown in the same colour. Sph, Sphingobium; Bac, Bacillus; Aci, Acinetobacter; Ter, Terribacillus; Cur, Curtobacterium; Pae, Paenibacillus; Pan, Pantoea; Rhi, Rhizobium; Chr, Chryseobacterium; Aer, Aerococcus; Art, Arthrobacter; Ste, Stenotrophomonas; Ach, Achromobacter; Pse, Pseudomonas; Can, Candidatus Cloacamonas; Agr, Agrobacterium; Bre, Brevundimonas; Ent, Enterococcus; Cau, Caulobacter; Dys, Dysgonomonas; Spb, Sphingobacterium; Ped, Pedobacter; Com, Comamonas; Oth, Other genera.

Figure 4

Chronological series of SEM images of the drip tray samples taken after 4 (A), 8 (B), 14 (C), and 21 days (D) of operation. Figure C corresponds to a sample highly abundant in Bacillus spp. Scale bars are indicated in each case.