Solutions in microbiome engineering: prioritizing barriers to organism establishment

Harnessing the plant microbiome for sustainable crop production

Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.

Biotechnological advances in plant growth-promoting rhizobacteria for sustainable agriculture

The rhizosphere, the soil zone surrounding plant roots, serves as a reservoir for numerous beneficial microorganisms that enhance plant productivity and crop yield, with substantial potential for application as biofertilizers. These microbes play critical roles in ecological processes such as nutrient recycling, organic matter decomposition, and mineralization. Plant growth-promoting rhizobacteria (PGPR) represent a promising tool for sustainable agriculture, enabling green management of crop health and growth, being eco-friendly alternatives to replace chemical fertilizers and pesticides. In this sense, biotechnological advancements respecting genomics and gene editing have been crucial to develop microbiome engineering which is pivotal in developing microbial consortia to improve crop production. Genome mining, which involves comprehensive analysis of the entire genome sequence data of PGPR, is crucial for identifying genes encoding valuable bacterial enzymes and metabolites. The CRISPR-Cas system, a cutting-edge genome-editing technology, has shown significant promise in beneficial microbial species. Advances in genetic engineering, particularly CRISPR-Cas, have markedly enhanced grain output, plant biomass, resistance to pests, and the sensory and nutritional quality of crops. There has been a great advance about the use of PGPR in important crops; however, there is a need to go further studying synthetic microbial communities, microbiome engineering, and gene editing approaches in field trials. This review focuses on future research directions involving several factors and topics around the use of PGPR putting special emphasis on biotechnological advances.

The contribution of beneficial wheat seed fungal communities beyond disease-causing fungi: Advancing heritable mycobiome-based plant breeding

Wheat (Triticum sp.) is a staple cereal crop, providing nearly a fifth of the world's protein and available calories. While fungi associated with wheat plants have been known for centuries, attention to fungi associated with wheat seeds has increased over the last hundred years. Initially, research focused on fungal taxa that cause seed-borne diseases. Seeds act as a physical link between generations and host specialized fungal communities that affect seed dormancy, germination, quality, and disease susceptibility. Interest in beneficial, non-disease-causing fungal taxa associated with seeds has grown since the discovery of Epichloë in fescue, leading to a search for beneficial fungal endophytes in cereal grains. Recent studies of the wheat seed mycobiome have shown that disease, seed development, and temporal variation significantly influence the composition and structure of these fungal communities. This research, primarily descriptive, aims to better understand the wheat seed mycobiome's function in relation to the plant host. A deeper understanding of the wheat seed mycobiome's functionality may offer potential for microbiome-assisted breeding.

Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review

Sustainable agriculture represents the responsible utilization of natural resources while safeguarding the well-being of the natural environment. It encompasses the objectives of preserving the environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize sustainable agriculture. One significant approach to achieving this transition is the extensive utilization of microbes, which play a crucial role due to the genetic reliance of plants on the beneficial functions provided by symbiotic microbes. This review focuses on the significance of rhizospheric microbial communities, also known as the rhizomicrobiome (RM). It is a complex community of microorganisms that live in the rhizosphere and influence the plant's growth and health. It provides its host plant with various benefits related to plant growth, including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, and other advantageous properties. Yet, the mechanisms by which the RM contributes to sustainable agriculture remain largely unknown. Investigating this microbial population presents a significant opportunity to advance toward sustainable agriculture. Hence, this study aims to provide an overview of the diversity and applications of RM in sustainable agriculture practices. Lately, there has been growing momentum in various areas related to rhizobiome research and its application in agriculture. This includes rhizosphere engineering, synthetic microbiome application, agent-based modeling of the rhizobiome, and metagenomic studies. So, developing bioformulations of these beneficial microorganisms that support plant growth could serve as a promising solution for future strategies aimed at achieving a new green revolution.

A strong priority effect in the assembly of a specialized insect-microbe symbiosis

Specialized host-microbe symbioses are ecological communities, whose composition is shaped by various processes. Microbial community assembly in these symbioses is determined in part by interactions between taxa that colonize ecological niches available within habitat patches. The outcomes of these interactions, and by extension the trajectory of community assembly, can display priority effects-dependency on the order in which taxa first occupy these niches. The underlying mechanisms of these phenomena vary from system to system and are often not well resolved. Here, we characterize priority effects in colonization of the squash bug (Anasa tristis) by bacterial symbionts from the genus Caballeronia, using pairs of strains that are known to strongly compete during host colonization, as well as strains that are isogenic and thus functionally identical. By introducing symbiont strains into individual bugs in a sequential manner, we show that within-host populations established by the first colonist are extremely resistant to invasion, regardless of strain identity and competitive interactions. By knocking down the population of an initial colonist with antibiotics, we further show that colonization success by the second symbiont is still diminished even when space in the symbiotic organ is available and ostensibly accessible for colonization. We speculate that resident symbionts exclude subsequent infections by manipulating the host environment, partially but not exclusively by eliciting tissue remodeling of the symbiont organ.

IMPORTANCE

Host-associated microbial communities underpin critical ecosystem processes and human health, and their ability to do so is determined in turn by the various processes that shape their composition. While selection deterministically acts on competing genotypes and species during community assembly, the manner by which selection determines the trajectory of community assembly can differ depending on the sequence by which taxa are established within that community. We document this phenomenon, known as a priority effect, during experimental colonization of a North American insect pest, the squash bug Anasa tristis, by its betaproteobacterial symbionts in the genus Caballeronia. Our study demonstrates how stark, strain-level variation can emerge in specialized host-microbe symbioses simply through differences in the order by which strains colonize the host. Understanding the mechanistic drivers of community structure in host-associated microbiomes can highlight both pitfalls and opportunities for the engineering of these communities and their constituent taxa for societal benefit.

Gut Akkermansia muciniphila, Prevotellaceae, and Enterobacteriaceae spp. as Possible Markers in Women-Related Nutritional and Clinical Trials: Familial Mediterranean Fever Disease

Background

Studies have shown that the gut microbiota of healthy men and men with familial Mediterranean fever (FMF) disease respond differently to placebo. Given the fact that the composition of the gut microbiota is different in men and women, this study aimed to describe in detail the placebo response of the gut microbiota in healthy and FMF women.

Materials and Methods

The bacterial response to placebo was fully evaluated on a previous PhyloChip™ DNA microarray-based assay (GEO Series; accession number GSE111835).

Results

The change in the total number of operational taxonomic units in healthy women exposed to placebo is more than that of healthy men, in contrast to FMF people (704 vs. 140 and 409 vs. 7560, respectively [p < 0.05]). Gut Firmicutes diversities are more sensitive to placebo, whereas Akkermansia muciniphila remained unchanged after the placebo administration for both healthy and FMF people. Gut Prevotellaceae and Enterobacteriaceae diversities of healthy subjects and FMF women are also almost unchanged from placebo. Meanwhile, only 56.35% of gut Enterobacteriaceae diversities in FMF men were placebo resistant.

Conclusion

The response to a placebo varies depending on a person's gender and health status. Healthy and FMF women's placebo study groups could be avoided by excluding placebo-sensitive 704 of 18,725 and 409 of 18,725 bacterial diversities, respectively. Because the placebo causes changes in all gut bacterial phyla in healthy and FMF women, and only the representatives of Enterobacteriaceae and Prevotellaceae families and A. muciniphila spp. are not affected by placebo, these bacteria can be considered as possible markers in women-related nutritional/clinical trials. Data on the response of the gut microbiota in healthy women to placebo might be used in studies of diseases other than FMF. The response of gut bacteria from different taxonomic affiliations to placebo may provide a basis for uncovering the role of these bacteria in the gut-brain axis.

The emerging role of the gut microbiota and its application in inflammatory bowel disease

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a complex disorder with an unknown cause. However, the dysbiosis of the gut microbiome has been found to play a role in IBD etiology, including exacerbated immune responses and defective intestinal barrier integrity. The gut microbiome can also be a potential biomarker for several diseases, including IBD. Currently, conventional treatments targeting pro-inflammatory cytokines and pathways in IBD-associated dysbiosis do not yield effective results. Other therapies that directly target the dysbiotic microbiome for effective outcomes are emerging. We review the role of the gut microbiome in health and IBD and its potential as a diagnostic, prognostic, and therapeutic target for IBD. This review also explores emerging therapeutic advancements that target gut microbiome-associated alterations in IBD, such as nanoparticle or encapsulation delivery, fecal microbiota transplantation, nutritional therapies, microbiome/probiotic engineering, phage therapy, mesenchymal stem cells (MSCs), gut proteins, and herbal formulas.

The early life microbiome of giant grouper (Epinephelus lanceolatus) larvae in a commercial hatchery is influenced by microorganisms in feed

Fish health, growth and disease is intricately linked to its associated microbiome. Understanding the influence, source and ultimately managing the microbiome, particularly for vulnerable early life-stages, has been identified as one of the key requirements to improving farmed fish production. One tropical fish species of aquaculture importance farmed throughout the Asia-Pacific region is the giant grouper (Epinephelus lanceolatus). Variability in the health and survival of E. lanceolatus larvae is partially dependent on exposure to and development of its early microbiome. Here, we examined the development in the microbiome of commercially reared giant grouper larvae, its surrounding environment, and that from live food sources to understand the type of bacterial species larvae are exposed to, and where some of the sources of bacteria may originate. We show that species richness and microbial diversity of the larval microbiome significantly increased in the first 4 days after hatching, with the community composition continuing to shift over the initial 10 days in the hatchery facility. The dominant larval bacterial taxa appeared to be predominantly derived from live cultured microalgae and rotifer feeds and included Marixanthomonas, Candidatus Hepatincola, Meridianimaribacter and Vibrio. In contrast, a commercial probiotic added as part of the hatchery's operating procedure failed to establish in the larvae microbiome. Microbial source tracking indicated that feed was the largest influence on the composition of the giant grouper larvae microbiome (up to 55.9%), supporting attempts to modulate fish microbiomes in commercial hatcheries through improved diets. The marked abundances of Vibrio (up to 21.7% of 16S rRNA gene copies in larvae) highlights a need for rigorous quality control of feed material.

Isolation and characterization of Septuagintavirus; a novel clade of Escherichia coli phages within the subfamily Vequintavirinae

Escherichia coli is a commensal inhabitant of the mammalian gut microbiota, frequently associated with various gastrointestinal diseases. There is increasing interest in comprehending the variety of bacteriophages (phages) that target this bacterium, as such insights could pave the way for their potential use in therapeutic applications. Here, we report the isolation and characterization of four newly identified E. coli infecting tailed phages (W70, A7-1, A5-4, and A73) that were found to constitute a novel genus, Septuagintavirus, within the subfamily Vequintavirinae. Genomes of these phages ranged from 137 kbp to 145 kbp, with a GC content of 41 mol%. They possess a maximum nucleotide similarity of 30% with phages of the closest phylogenetic genus, Certrevirus, while displaying limited homology to other genera of the Vequintavirinae family. Host range analysis showed that these phages have limited activity against a panel of E. coli strains, infecting 6 out of 16 tested isolates, regardless of their phylotype. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was performed on the virion of phage W70, allowing the identification of 28 structural proteins, 19 of which were shared with phages of other genera of Vequintavirinae family. The greatest diversity was identified with proteins forming tail fiber structures, likely indicating the adaptation of virions of each phage genus of this subfamily for the recognition of their target receptor on host cells. The findings of this study provide greater insights into the phages of the subfamily Vequintavirinae, contributing to the pool of knowledge currently known about these phages.

IMPORTANCE

Escherichia coli is a well-known bacterium that inhabits diverse ecological niches, including the mammalian gut microbiota. Certain strains are associated with gastrointestinal diseases, and there is a growing interest in using bacteriophages, viruses that infect bacteria, to combat bacterial infections. Here, we describe the isolation and characterization of four novel E. coli bacteriophages that constitute a new genus, Septuagintavirus, within the subfamily Vequintavirinae. We conducted mass spectrometry on virions of a representative phage of this novel clade and compared it to other phages within the subfamily. Our analysis shows that virion structure is highly conserved among all phages, except for proteins related to tail fiber structures implicated in the host range. These findings provide greater insights into the phages of the subfamily Vequintavirinae, contributing to the existing pool of knowledge about these phages.

Degradation of polyethylene terephthalate (PET) plastics by wastewater bacteria engineered via conjugation

Wastewater treatment plants are one of the major pathways for microplastics to enter the environment. In general, microplastics are contaminants of global concern that pose risks to ecosystems and human health. Here, we present a proof-of-concept for reduction of microplastic pollution emitted from wastewater treatment plants: delivery of recombinant DNA to bacteria in wastewater to enable degradation of polyethylene terephthalate (PET). Using a broad-host-range conjugative plasmid, we enabled various bacterial species from a municipal wastewater sample to express FAST-PETase, which was released into the extracellular environment. We found that FAST-PETase purified from some transconjugant isolates could degrade about 40% of a 0.25 mm thick commercial PET film within 4 days at 50°C. We then demonstrated partial degradation of a post-consumer PET product over 5-7 days by exposure to conditioned media from isolates. These results have broad implications for addressing the global plastic pollution problem by enabling environmental bacteria to degrade PET.

Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization

Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping, which consists of using part of the previous production to inoculate a new one, can be used as a model engineering approach to investigate community dynamics during serial propagations. In this study, 26 raw milk samples were serially propagated 6 times each, giving rise to 26 community lineages. Bacterial community structures were analyzed by metabarcoding, and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high variability of structure and diverse acidification properties between community lineages. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure.

IMPORTANCE

Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy backslopping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.

DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories

BACKGROUND

Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation.

RESULTS

Inoculation effectively increased PAH removal in the short-term, but not in the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil.

CONCLUSION

Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.

Understanding the Role of Controlled Environments for Producing Mycelium-bound Composites: Advancing Circular Practices for Integrating Biotechnology into the Construction Industry

The architecture, engineering, and construction industry is undergoing a significant shift, steering buildings away from resource-intensive processes toward becoming instruments for climate mitigation. In this transformative landscape, integrating circular bio-based alternatives and reducing emissions through biotechnological and enzymatic processes have significant potential. Specifically, mycelium-bound composites have emerged as renewable alternatives for new materials and added-value wood products. Despite their numerous advantages, integrating these materials into current engineering practices presents challenges deriving from the complex nature of the material´s production process and the transfer from the laboratory to the industrial scale. In this regard, the design and engineering of novel controlled environments are fundamental in maintaining optimal growth conditions during material production. This, in turn, influences the overall material performance and potential use in construction.

Use of zebrafish to identify host responses specific to type VI secretion system mediated interbacterial antagonism

Interbacterial competition is known to shape the microbial communities found in the host, however the interplay between this competition and host defense are less clear. Here, we use the zebrafish hindbrain ventricle (HBV) as an in vivo platform to investigate host responses to defined bacterial communities with distinct forms of interbacterial competition. We found that antibacterial activity of the type VI secretion system (T6SS) from both Vibrio cholerae and Acinetobacter baylyi can induce host inflammation and sensitize the host to infection independent of any individual effector. Chemical suppression of inflammation could resolve T6SS-dependent differences in host survival, but the mechanism by which this occurred differed between the two bacterial species. By contrast, colicin-mediated antagonism elicited by an avirulent strain of Shigella sonnei induced a negligible host response despite being a more potent bacterial killer, resulting in no impact on A. baylyi or V. cholerae virulence. Altogether, these results provide insight into how different modes of interbacterial competition in vivo affect the host in distinct ways.

Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues

Parallel to the important use of pesticides in conventional agriculture there is a growing interest for green technologies to clear contaminated soil from pesticides and their degradation products. Bioaugmentation i. e. the inoculation of degrading micro-organisms in polluted soil, is a promising method still in needs of further developments. Specifically, improvements in the understanding of how degrading microorganisms must overcome abiotic filters and interact with the autochthonous microbial communities are needed in order to efficiently design bioremediation strategies. Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY) and isoproturon (IPU), via experimental modifications of two source bacterial communities. We used statistical methods stemming from genomic prediction to link community composition to herbicides degradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 - between model predictions and measured pesticide degradation values. Multi-degrading bacterial communities were obtained by coalescing bacterial communities with high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated the efficiency of constructed multi-degrading communities to remove pesticide contamination in a different soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading capacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether, we developed an innovative protocol for building multi-degrading simplified bacterial communities with the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.

Unlocking bacterial potential to reduce farmland N2O emissions

Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.

Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation

Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.

Quorum sensing bacteria improve microbial networks stability and complexity in wastewater treatment plants

Quorum-sensing bacteria (QSB) are crucial factors for microbial communication, yet their ecological role in wastewater treatment plants (WWTPs) remains unclear. Here, we developed a method to identify QSB by comparing 16S rRNA gene sequences. QSB in 388 activated sludge samples collected from 130 WWTPs across China primarily were identified as rare taxa and conditionally rare taxa. A co-occurrence network shared by all sludge communities revealed that QSB exhibited higher average clustering coefficient (0.46) than non-QSB (0.15). Individual sludge networks demonstrated that quorum sensing microbiomes were positively correlated with network robustness and network complexity, including average clustering coefficient and link density. We confirmed that QSB keystones and QSB nodes have a positive impact on network complexity by influencing network modularity through a structural equation model. Meanwhile, QSB communities directly contributed to maintaining network robustness (r = 0.29, P < 0.05). Hence, QSB play an important role in promoting network complexity and stability. Furthermore, QSB communities were positively associated with the functional composition of activated sludge communities (r = 0.33, P < 0.01), especially the denitrification capacity (r = 0.45, P < 0.001). Overall, we elucidated the ecological significance of QSB and provided support for QS-based regulation of activated sludge microbial communities.

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship

The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions

Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.

The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2024;43:637-652. © 2022 SETAC.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Soil microbiome analysis supports claims of ineffectiveness of Pseudomonas fluorescens D7 as a biocontrol agent of Bromus tectorum

IMPORTANCE

Cheatgrass is one of North America's most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P. fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens at 18 months post-application.

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass

Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted.

ONE-SENTENCE SUMMARY

This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.

Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system

Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.

Niche differentiation in microbial communities with stable genomic traits over time in engineered systems

Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.

Microbiota and glioma: a new perspective from association to clinical translation

Gliomas pose a significant challenge in oncology due to their malignant nature, aggressive growth, frequent recurrence, and complications posed by the blood-brain barrier. Emerging research has revealed the critical role of gut microbiota in influencing health and disease, indicating its possible impact on glioma pathogenesis and treatment responsiveness. This review focused on existing evidence and hypotheses on the relationship between microbiota and glioma from progression to invasion. By discussing possible mechanisms through which microbiota may affect glioma biology, this paper offers new avenues for targeted therapies and precision medicine in oncology.

Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning

Plant-associated microbiomes contribute to important ecosystem functions such as host resistance to biotic and abiotic stresses. The factors that determine such community outcomes are inherently difficult to identify under complex environmental conditions. In this study, we present an experimental and analytical approach to explore microbiota properties relevant for a microbiota-conferred host phenotype, here plant protection, in a reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification and regression analyses as well as empirical validation to test potential explanatory factors of community structure and composition, including evenness, total commensal colonization, phylogenetic diversity, and strain identity. We find strain identity to be the most important predictor of pathogen reduction, with machine learning algorithms improving performances compared to random classifications (94-100% versus 32% recall) and non-modelled predictions (0.79-1.06 versus 1.5 RMSE). Further experimental validation confirms three strains as the main drivers of pathogen reduction and two additional strains that confer protection in combination. Beyond the specific application presented in our study, we provide a framework that can be adapted to help determine features relevant for microbiota function in other biological systems.

The seed microbiomes of staple food crops

The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.

Harnessing biological nitrogen fixation in plant leaves

The importance of biological nitrogen fixation (BNF) in securing food production for the growing world population with minimal environmental cost has been increasingly acknowledged. Leaf surfaces are one of the biggest microbial habitats on Earth, harboring diverse free-living N2-fixers. These microbes inhabit the epiphytic and endophytic phyllosphere and contribute significantly to plant N supply and growth. Here, we summarize the contribution of phyllosphere-BNF to global N cycling, evaluate the diversity of leaf-associated N2-fixers across plant hosts and ecosystems, illustrate the ecological adaptation of N2-fixers to the phyllosphere, and identify the environmental factors driving BNF. Finally, we discuss potential BNF engineering strategies to improve the nitrogen uptake in plant leaves and thus sustainable food production.

Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra

Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.

Microbiome modulation in inflammatory diseases: Progress to microbiome genetic engineering

Recent developments in sequencing technology and analytical approaches have allowed researchers to show that the healthy gut microbiome is very varied and capable of performing a wide range of tasks. The importance of gut microbiota in controlling immunological, neurological, and endocrine function is becoming well-recognized. Thereby, numerous inflammatory diseases, including those that impact the gastrointestinal system, as well as less obvious ones, including Rheumatoid arthritis (RA), cancer, gestational diabetes (GD), type 1 diabetes (T1D), and type 2 diabetes (T2D), have been linked to dysbiotic gut microbiota. Microbiome engineering is a rapidly evolving frontier for solutions to improve human health. Microbiome engineering seeks to improve the function of an ecosystem by manipulating the composition of microbes. Thereby, generating potential therapies against metabolic, inflammatory, and immunological diseases will be possible through microbiome engineering. This essay first provides an overview of the traditional technological instruments that might be used for microbiome engineering, such as Fecal Microbiota Transplantation (FMT), prebiotics, and probiotics. Moreover, we will also discuss experimental genetic methods such as Metagenomic Alteration of Gut microbiome by In situ Conjugation (MAGIC), Bacteriophage, and Conjugative plasmids in manipulating intestinal microbiota.

Deconstructing taxa x taxa xenvironment interactions in the microbiota: A theoretical examination

A major objective of microbial ecology is to identify how the composition of microbial taxa shapes host phenotypes. However, most studies focus on pairwise interactions and ignore the potentially significant effects of higher-order microbial interactions.Here, we quantify the effects of higher-order interactions among taxa on host infection risk. We apply our approach to an in silico dataset that is built to resemble a population of insect hosts with gut-associated microbial communities at risk of infection from an intestinal parasite across a breadth of nutrient environmental contexts.We find that the effect of higher-order interactions is considerable and can change appreciably across environmental contexts. Furthermore, we show that higher-order interactions can stabilize community structure thereby reducing host susceptibility to parasite invasion.Our approach illustrates how incorporating the effects of higher-order interactions among gut microbiota across environments can be essential for understanding their effects on host phenotypes.

Deep insight into oriented propionate production from food waste: Microbiological interpretation and design practice

Using mixed microbial cultures (MMCs) for oriented volatile fatty acids (VFAs) refining in an open environment is a typical challenge due to the microbial diversiform and the process complexity. Especially for carbohydrate-rich waste (such as food waste), butyrate-type fermentation is usually dominant in a single-stage MMCs anaerobic process, while the production of odd-carbon VFAs (such as propionate) is difficult although it plays a significant role in chemicals industries. In this study, firstly, we gave a new perspective on the rationality of the oriented propionate production using MMCs with lactate as feedstock by conducting in-depth microbial informatics and reaction analysis. Secondly, we verified the feasibility of the "food waste-lactate-propionate" route to reverse the original butyrate-type fermentation situation and explore mechanisms for maintaining stability. In the first stage, a defined lactate fermentation microbiome was used to produce lactate-containing broth (80% of total chemical oxygen demand) at pH=4. In the second stage, an undomesticated undefined anaerobic microbiome was used to drive propionate production (45.26% ± 2.23% of total VFAs) under optimized conditions (C/N = 100:1-200:1 and pH=5.0). The low pH environment in the first stage enhanced the lactic acid bacteria to resist the invasion of non-functional flanking bacteria, making the community stable. In the second stage, the system maintained the propionate-type fermentation due to the absence of the ecological niche of the invasive lactic acid bacteria; The selection of propionate-producing specialists was a necessary but not sufficient condition for propionate-type fermentation. At last, this study proposed an enhanced engineering strategy framework for understanding elaborate MMCs fermentation.

Ecological principles of fecal microbiota transplantation

Fecal microbiota transplantation (FMT) is a procedure used to treat diseases related to microbiome imbalances. We discuss how ecological principles can inform the design of FMT clinical trials and contribute to data interpretation. This effort will promote a better understanding of microbiome engraftment and assist the development of clinical protocols.

Microbiome rescue: directing resilience of environmental microbial communities

Earth's climate crisis threatens to disrupt ecosystem services and destabilize food security. Microbiome management will be a crucial component of a comprehensive strategy to maintain stable microbinal functions for ecosystems and plants in the face of climate change. Microbiome rescue is the directed, community-level recovery of microbial populations and functions lost after an environmental disturbance. Microbiome rescue aims to propel a resilience trajectory for community functions. Rescue can be achieved via demographic, functional, adaptive, or evolutionary recovery of disturbance-sensitive populations. Various ecological mechanisms support rescue, including dispersal, reactivation from dormancy, functional redundancy, plasticity, and diversification, and these mechanisms can interact. Notably, controlling microbial reactivation from dormancy is a potentially fruitful but underexplored target for rescue.

The potential of tailoring the gut microbiome to prevent and treat cardiometabolic disease

Despite milestones in preventive measures and treatment, cardiovascular disease (CVD) remains associated with a high burden of morbidity and mortality. The protracted nature of the development and progression of CVD motivates the identification of early and complementary targets that might explain and alleviate any residual risk in treated patients. The gut microbiota has emerged as a sentinel between our inner milieu and outer environment and relays a modified risk associated with these factors to the host. Accordingly, numerous mechanistic studies in animal models support a causal role of the gut microbiome in CVD via specific microbial or shared microbiota-host metabolites and have identified converging mammalian targets for these signals. Similarly, large-scale cohort studies have repeatedly reported perturbations of the gut microbial community in CVD, supporting the translational potential of targeting this ecological niche, but the move from bench to bedside has not been smooth. In this Review, we provide an overview of the current evidence on the interconnectedness of the gut microbiome and CVD against the noisy backdrop of highly prevalent confounders in advanced CVD, such as increased metabolic burden and polypharmacy. We further aim to conceptualize the molecular mechanisms at the centre of these associations and identify actionable gut microbiome-based targets, while contextualizing the current knowledge within the clinical scenario and emphasizing the limitations of the field that need to be overcome.

The microbiome of cereal plants: The current state of knowledge and the potential for future applications

The plant microbiota fulfils various crucial functions related to host health, fitness, and productivity. Over the past years, the number of plant microbiome studies continued to steadily increase. Technological advancements not only allow us to produce constantly increasing datasets, but also to extract more information from them in order to advance our understanding of plant-microbe interactions. The growing knowledge base has an enormous potential to improve microbiome-based, sustainable agricultural practices, which are currently poorly understood and have yet to be further developed. Cereal plants are staple foods for a large proportion of the world's population and are therefore often implemented in microbiome studies. In the present review, we conducted extensive literature research to reflect the current state of knowledge in terms of the microbiome of the four most commonly cultivated cereal plants. We found that currently the majority of available studies are targeting the wheat microbiome, which is closely followed by studies on maize and rice. There is a substantial gap, in terms of published studies, addressing the barley microbiome. Overall, the focus of most microbiome studies on cereal plants is on the below-ground microbial communities, and there is more research on bacteria than on fungi and archaea. A meta-analysis conducted in the frame of this review highlights microbiome similarities across different cereal plants. Our review also provides an outlook on how the plant microbiota could be harnessed to improve sustainability of cereal crop production.

The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?

Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe–plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host–microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.

Microbes to support plant health: understanding bioinoculant success in complex conditions

A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for plant performance and health. When applied in agriculture to improve crop yield and performance, these microbes are commonly referred to as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically in the field, hampering their applicability. Invasion of the rhizosphere microbiome is a critical determinant for bioinoculant success. Invasion is a complex phenomenon that is shaped by interactions with the local, resident microbiome and the host plant. Here, we explore all of these dimensions by cross-cutting ecological theory and molecular biology of microbial invasion in the rhizosphere. We refer to the famous Chinese philosopher and strategist Sun Tzu, who believed that solutions for problems require deep understanding of the problems themselves, to review the major biotic factors determining bioinoculant effectiveness.

Microbiome engineering for bioremediation of emerging pollutants

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

The Use of Probiotics during Rearing of Hermetia illucens: Potential, Caveats, and Knowledge Gaps

Given the novelty of the industrial production of the edible insects sector, research has primarily focused on the zootechnical performances of black soldier fly larvae (BSFL) in response to different substrates and rearing conditions as a basis to optimize yield and quality. However recently, research has started to focus more on the associated microbes in the larval digestive system and their substrates and the effect of manipulating the composition of these communities on insect performance as a form of microbiome engineering. Here we present an overview of the existing literature on the use of microorganisms during rearing of the BSFL to optimize the productivity of this insect. These studies have had variable outcomes and potential explanations for this variation are offered to inspire future research that might lead to a better success rate for microbiome engineering in BSFL.

Computational design of CRISPR guide RNAs to enable strain-specific control of microbial consortia

Microbes naturally coexist in complex, multistrain communities. However, extracting individual microbes from and specifically manipulating the composition of these consortia remain challenging. The sequence-specific nature of CRISPR guide RNAs can be leveraged to accurately differentiate microorganisms and facilitate the creation of tools that can achieve these tasks. We developed a computational program, ssCRISPR, which designs strain-specific CRISPR guide RNA sequences with user-specified target strains, protected strains, and guide RNA properties. We experimentally verify the accuracy of the strain specificity predictions in both Escherichia coli and Pseudomonas spp. and show that up to three nucleotide mismatches are often required to ensure perfect specificity. To demonstrate the functionality of ssCRISPR, we apply computationally designed CRISPR-Cas9 guide RNAs to two applications: the purification of specific microbes through one- and two-plasmid transformation workflows and the targeted removal of specific microbes using DNA-loaded liposomes. For strain purification, we utilize gRNAs designed to target and kill all microbes in a consortium except the specific microbe to be isolated. For strain elimination, we utilize gRNAs designed to target only the unwanted microbe while protecting all other strains in the community. ssCRISPR will be of use in diverse microbiota engineering applications.

Temperate bacteriophages infecting the mucin-degrading bacterium Ruminococcus gnavus from the human gut

Ruminococcus gnavus is a prevalent gut microbe reported to occur in higher abundance among individuals with inflammatory bowel disease (IBD). This study reports the isolation and characterization of six bacteriophages (phages) isolated from human fecal material and environmental samples that infect this species. Isolated phages have a siphovirus morphology, with genomes ranging between 36.5 and 37.8 kbp. Genome analysis indicates that the phages have a temperate lifestyle, which was confirmed by their ability to form lysogens on their host bacterial species. In contrast to the finding that phages lyse their host in liquid medium, results from a mouse trial indicate these phages can co-exist with the host bacterium in the gut without causing a significant reduction of R. gnavus. The bacterial counts in the feces of phage-treated mice did not significantly differ in the presence of phage. Furthermore, analysis of publicly available gut virome sequence data indicates a high abundance of these phages among individuals suffering from IBD. This work provides the first insight into how phages interact with R. gnavus in the human gut microbiome.

Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants

For over a century, physicians have witnessed a common enrichment of bifidobacteria in the feces of breast-fed infants that was readily associated with infant health status. Recent advances in bacterial genomics, metagenomics, and glycomics have helped explain the nature of this unique enrichment and enabled the tailored use of probiotic supplementation to restore missing bifidobacterial functions in at-risk infants. This review documents a 20-year span of discoveries that set the stage for the current use of human milk oligosaccharide-consuming bifidobacteria to beneficially colonize, modulate, and protect the intestines of at-risk, human milk-fed, neonates. This review also presents a model for probiotic applications wherein bifidobacterial functions, in the form of colonization and HMO-related catabolic activity in situ, represent measurable metabolic outcomes by which probiotic efficacy can be scored toward improving infant health.

Impact of Plant-Beneficial Bacterial Inocula on the Resident Bacteriome: Current Knowledge and Future Perspectives

The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading to increased plant biomass and yield and improved plant health, as well as the ameliorated nutritional value of fruits and edible seeds. During the last decades, exciting, but heterogeneous, results have been obtained growing PGPB inoculated plants under controlled, stressful, and open field conditions. On the other hand, the possible impact of the PGPB deliberate release on the resident microbiota has been less explored and the little available information is contradictory. This review aims at filling this gap: after a brief description of the main mechanisms used by PGPB, we focus our attention on the process of PGPB selection and formulation and we provide some information on the EU regulation for microbial inocula. Then, the concept of PGPB inocula as a tool for rhizosphere engineering is introduced and the possible impact of bacterial inoculant on native bacterial communities is discussed, focusing on those bacterial species that are included in the EU regulation and on other promising bacterial species that are not yet included in the EU regulation.

Plant Microbiome Engineering: Hopes or Hypes

Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.

Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use

Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.

Methods of DNA introduction for the engineering of commensal microbes

The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes. Over the past decades, the accumulated observational evidence reveals a close correlation between the microbiome and human health and disease. Many groups are now manipulating individual microbial strains, species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome. Here, we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria, including transformation, transduction, and conjugation. We provide an overview of these approaches and describe the advantages and limitations of each method. In addition, we highlight examples of human microbiome engineering using these approaches. Finally, we provide perspectives for the future of microbiome engineering.