Abstract: A method for automated, high throughput cellular library generation is disclosed. The method includes providing a suspension including transformed cells and plating the transformed cells onto solid surfaces of each of at least one reservoir of a reservoir plate. The solid surfaces can include a liquid growth medium. The reservoir plate is incubated, and after cellular growth has occurred on at least one plated surface of the reservoir plate, a series of automatic steps are performed. The automatically-performed steps include adding disaggregation solution to the reservoir plate, applying a mechanical force, such as a rotational force, to the reservoir plate to produce resuspended cells, and/or collecting the resuspended cells.

Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.

Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.

Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.

Abstract: HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods can be carried out within optofluidic devices.

Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.

Abstract: The present invention relates to methods for editing the genome of a microbial host cell in one or more rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in a pooled and/or iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Compositions and kits for performing the methods are also disclosed.

Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.

Abstract: Aspects of this disclosure relate to liquid-based workflows for strain engineering. In strain engineering, cells undergo a modification process to acquire a desired change or changes in the cells. Some of the cells accept the change or changes and some do not. Provided herein are liquid-based methods for selecting the population of cells that have accepted the change or changes. Also provided herein are liquid-based methods for removing markers from transformed cells and liquid-based methods for isolating clonally pure populations of cells.

Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.

Abstract: The present invention relates to methods for editing the genome of a microbial host cell in one or more rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in a pooled and/or iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Compositions and kits for performing the methods are also disclosed.

Abstract: The present invention relates to methods for genotyping microbial host cells that have been subjected to metabolic engineering. The methods provided herein allow detection of genetic edits in the genome of a microbial host cell using PCR-based genome enrichment following appendage of a common priming site. The compositions and methods of the present invention can be used to confirm engineered metabolic diversity as well as ectopic insertions. Kits for performing the methods are also disclosed.

Abstract: Compositions and methods using shufflon recombinases are presented for use in generating genetic diversity in molecules of interest.

Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.

Abstract: Provided herein are synthetic pathways from Escherichia coli and Vibrio cholerae genes for the production of new, synthetic nonribosomal peptides, and methods and compositions comprising the same. Some aspects of the present disclosure are directed to modified bacterial cells comprising a compressed biosynthetic pathway that comprises (a) biosynthetic genes obtained from one species encoding enzymes active in the bioassembly of a nonribosomal molecule, (b) biosynthetic genes obtained from another species encoding enzymes active in the bioassembly of a nonribosomal molecule that is different from the nonribosomal molecule of (a). In some embodiments, the biosynthetic genes of (a) are Escherichia coli biosynthetic genes and may include entD gene, an entC gene, an entE gene, an entB gene and an entA gene. In some embodiments, the biosynthetic genes of (b) are Vibrio cholera biosynthetic genes and may include a vibH gene and a vibF gene.

Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.

Abstract: The present invention relates to methods for editing the genome of a microbial host cell in one or more rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in a pooled and/or iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Compositions and kits for performing the methods are also disclosed.

Abstract: The present disclosure provides a HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition.

Abstract: Aspects of this disclosure relate to liquid-based workflows for strain engineering. In strain engineering, cells undergo a modification process to acquire a desired change or changes in the cells. Some of the cells accept the change or changes and some do not. Provided herein are liquid-based methods for selecting the population of cells that have accepted the change or changes. Also provided herein are liquid-based methods for removing markers from transformed cells and liquid-based methods for isolating clonally pure populations of cells.

Abstract: Compositions and methods using shufflon recombinases are presented for use in generating genetic diversity in molecules of interest.