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ABSTRACT Sourdough starters are spontaneously generated multispecies communities consisting of lactic acid bacteria (LAB) and yeasts. Traditionally used to make baked goods, these communities of microorganisms can be propagated through successive transfers to other containers. Successive transfers result in microbial community dynamics; however, the mechanisms guiding the dynamics are not fully elucidated. This study tracked five species of sourdough LAB-yeast communities (three LAB species and two yeast species) during successive transfers in vitro to explore the interspecies interactions driving the multispecies community dynamics. The microbial dynamics were modeled with a generalized Lotka–Volterra (gLV) equation, which can mathematically identify ecological types of interspecies interactions. The gLV model simulated the population dynamics of each species with Pearson’s correlation coefficient values of ≥0.817. Pairwise experiments revealed that competition (negative/negative) predominated among all pairwise interactions (70%), followed by amensalism (negative/neutral) (30%). In the pairwise community, the LAB species Limosilactobacillus fermentum suppressed Saccharomyces cerevisiae growth through amensalism; however, S. cerevisiae population was maintained when the community comprised 3–5 species, including the LAB species L. fermentum and Pediococcus pentosaceus. The key interspecies interactions for maintaining the S. cerevisiae population were theoretically determined using the gLV model; the three identified species interacted non-transitively with S. cerevisiae in a cyclic pairwise interaction, metaphorically representing a rock–paper–scissors relationship, which systemically supported the S. cerevisiae population in the multispecies community. These theoretical insights indicate that cyclic pairwise interaction is the main driver of LAB-yeast population dynamics, which helps sustain a vulnerable yeast species in a sourdough multispecies community. IMPORTANCE Traditionally, multispecies consisting of lactic acid bacteria and yeasts collaboratively engage sourdough fermentation, which determines the quality of the resulting baked goods. Nonetheless, the successive transfer of these microbial communities can result in undesirable community dynamics that prevent the formation of high-quality sourdough bread. Thus, a mechanistic understanding of the community dynamics is fundamental to engineer sourdough complex fermentation. This study describes the population dynamics of five species of lactic acid bacteria-yeast communities in vitro using a generalized Lotka–Volterra model that examines interspecies interactions. A vulnerable yeast species was maintained within up to five species community dynamics by obtaining support with a cyclic interspecies interaction. Metaphorically, it involves a rock–paper–scissors game between two lactic acid bacteria species. Application of the generalized Lotka–Volterra model to real food microbiomes including sourdoughs will increase the reliability of the model prediction and help identify key microbial interactions that drive microbiome dynamics.

ABSTRACT This study details a unique process of autothermal thermophilic aerobic digestion (ATAD) of human excreta useful in producing nitrogen-rich and pathogen-free organic fertilizer. The process was divided into initial, middle, and final phases, based on changes in temperature, dissolved oxygen (DO), and bacterial community structure. The aim of this study was to determine bacterial factors that would affect liquid fertilizer production in the process, using shotgun metagenomic analysis of each phase. Although the abundances of all 28 gene categories include 4 categories in SEED subsystems level 1 were similar to those in another type of wastewater treatment system, the abundances of 4 gene categories changed remarkably. Among them, a decrease in the abundance of the phage-related gene category and the presence of antibacterial substances in secondary metabolism may explain the change in bacterial community structure from the material to the initial phase. Increases in the abundances of two gene categories, phage-related and secondary metabolism, coincided with a decrease in alpha diversity from the material to the initial phase. A potential increase in the abundance of genes in the category of sporulation from the middle to the final phase was correlated with deterioration of growth conditions and stabilization processes. In addition, prompt consumption of short-chain fatty acids in the initial phase and unusually stable ammonia accumulation throughout the process could be explained by the presence/absence of related metabolic genes. In conclusion, the relationships between bacterial function and unique characteristics of ATAD were revealed; our findings support the enhancement of liquid fertilizer production from wastewater. IMPORTANCE Metagenome analysis was performed to determine the microbial dynamics of the unique autothermal thermophilic aerobic digestion process of human excreta, which includes initial, middle, and final phases. In this study, we revealed the details of functional genes related to physicochemical and bacterial characteristics in the ATAD process. Four gene categories showed increases and decreases during the digestion process. In addition, the unusual stable accumulation of ammonia and prompt consumption of short-chain fatty acids were explained by the absence or presence of related metabolic genes. In addition to revealing the relationships between bacteria and physicochemical properties, the results of this research may support improving wastewater management systems worldwide by using the ATAD process in liquid fertilizer production systems.

A unique autothermal thermophilic aerobic digestion (ATAD) process has been used to convert human excreta to liquid fertilizer in Japan. This study investigated the changes in physicochemical and bacterial community characteristics during the full-scale ATAD process operated for approximately 3 weeks in 2 different years. After initiating simultaneous aeration and mixing using an air-inducing circulator (aerator), the temperature autothermally increased rapidly in the first 1 to 2 days with exhaustive oxygen consumption, leading to a drastic decrease and gradual increase in oxidation-reduction potential in the first 2 days, reached >50°C in the middle 4 to 6 days, and remained steady in the final phase. Volatile fatty acids were rapidly consumed and diminished in the first 2 days, whereas the ammonia nitrogen concentration was relatively stable during the process, despite a gradual pH increase to 9.3. Principal-coordinate analysis of 16S rRNA gene amplicons using next-generation sequencing divided the bacterial community structures into distinct clusters corresponding to three phases, and they were similar in the final phase in both years despite different transitions in the middle phase. The predominant phyla (closest species, dominancy) in the initial, middle, and final phases were Proteobacteria (Arcobacter trophiarum, 19 to 43%; Acinetobacter towneri, 6.3 to 30%), Bacteroidetes (Moheibacter sediminis, 43 to 54%), and Firmicutes (Thermaerobacter composti, 11 to 28%; Heliorestis baculata, 2.1 to 16%), respectively. Two predominant operational taxonomic units (OTUs) in the final phase showed very low similarities to the closest species, indicating that the process is unique compared with previously published ones. This unique process with three distinctive phases would be caused by the aerator with complete aeration. [ABSTRACT FROM AUTHOR]