The present invention provides for novel metabolic pathways to convert biomass and other carbohydrate sources to malonyl-CoA derived products, such as hydrocarbons and other bioproducts, under anaerobic conditions and with the net production of ATP. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to achieve conversion of a carbohydrate source to, e.g., long-chain hydrocarbons and hydrocarbon derivatives, wherein the one or more native and/or heterologous enzymes is activated, upregulated, downregulated, or deleted. The invention also provides for processes to convert biomass to malonyl-CoA derived products which comprise contacting a carbohydrate source with a recombinant microorganism of the invention.

The present invention provides for novel metabolic pathways to convert biomass and other carbohydrate sources to malonyl-CoA derived products, such as hydrocarbons and other bioproducts, under anaerobic conditions and with the net production of ATP. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to achieve conversion of a carbohydrate source to, e.g., long-chain hydrocarbons and hydrocarbon derivatives, wherein the one or more native and/or heterologous enzymes is activated, upregulated, downregulated, or deleted. The invention also provides for processes to convert biomass to malonyl-CoA derived products which comprise contacting a carbohydrate source with a recombinant microorganism of the invention.

Isolated cellulolytic extreme thermophilic bacterial cells belonging to the genus Caldicellulosiruptor, mutants thereof, isolated strains, microbial cultures and microbial compositions. The novel bacteria are in particular suitable for the production of fermentation products such as lactic acid from any carbon source, not limited to cellulosic material but especially useful for converting cellulosic biomass like lignocellulosic biomass and/or starch containing biomass.

Isolated cellulolytic extreme thermophilic bacterial cells belonging to the genus Caldicellulosiruptor, mutants thereof, isolated strains, microbial cultures and microbial compositions. The novel bacteria are in particular suitable for the production of fermentation products such as lactic acid from any carbon source, not limited to cellulosic material but especially useful for converting cellulosic biomass like lignocellulosic biomass and/or starch containing biomass.

A cell separation and culture device having a porous substrate; and a patterned carbon powder layer having a plurality of hollow regions, formed on an upper surface of the porous substrate by a forming manner; wherein the thickness of the patterned carbon powder layer is 0.04-0.08 mm. The cell separation and culture device is able to separate, detect or culture cells with various size and shape. The cell separation and culture device of present invention also simplifies the process of cell separation, detection and culture; therefore, it is accomplished within a very short time.

A cell separation and culture device having a porous substrate; and a patterned carbon powder layer having a plurality of hollow regions, formed on an upper surface of the porous substrate by a forming manner; wherein the thickness of the patterned carbon powder layer is 0.04-0.08 mm. The cell separation and culture device is able to separate, detect or culture cells with various size and shape. The cell separation and culture device of present invention also simplifies the process of cell separation, detection and culture; therefore, it is accomplished within a very short time.

Embodiments provide a modified microbe capable of growing in or fermenting a solution, or lignocellulosic hydrolysate, comprising ferulic acid and/or coniferyl aldehyde. The microbe has one or more modifications to provide: (a) a decrease in copy number or expression of a BNA7 gene; (b) an increase in copy number or expression of one or more pentose phosphate pathway genes; and/or (c) localization of one or more products of the pentose phosphate pathway genes to the mitochondria or endoplasmic reticulum. Also provided is a microbe having modified expression or copy number of BNA7 and/or one or more of the pentose phosphate pathway genes. The pentose phosphate pathway genes may in certain embodiments be selected from at least one of ZWF1, TKL1, RPE1 and GND1. Also provided is a method for fermenting a substrate comprising ferulic acid and/or coniferyl aldehyde to produce a fermentation product.

Provided herein are methods of making microorganisms modified for increased xylose consumption as compared to unmodified microorganisms. The methods include providing xylose-consuming microorganisms comprising two or more copies of a nucleic acid sequence encoding xylose isomerase and two or more copies of a nucleic acid sequence encoding a xylose kinase, culturing the microorganisms in medium containing xylose and harvesting a portion of the microorganisms. These steps are repeated multiple times. The microorganisms are then isolated. The isolated microorganisms have increased xylose consumption rates compared to control xylose-consuming microorganisms. Also provided are a population of microorganisms made by the provided methods. Methods of culturing the population of microorganisms and methods of reducing xylitol production in cultures comprising the population of microorganisms are provided.

Provided herein are methods of making microorganisms modified for increased xylose consumption as compared to unmodified microorganisms. The methods include providing xylose-consuming microorganisms comprising two or more copies of a nucleic acid sequence encoding xylose isomerase and two or more copies of a nucleic acid sequence encoding a xylose kinase, culturing the microorganisms in medium containing xylose and harvesting a portion of the microorganisms. These steps are repeated multiple times. The microorganisms are then isolated. The isolated microorganisms have increased xylose consumption rates compared to control xylose-consuming microorganisms. Also provided are a population of microorganisms made by the provided methods. Methods of culturing the population of microorganisms and methods of reducing xylitol production in cultures comprising the population of microorganisms are provided.

The invention relates to a method for preparing a yeast which is capable of simultaneously fermenting a pentose and a hexose sugar, the method comprising providing a yeast which comprises: one or more heterologous genes encoding an enzyme of a pentose metabolic pathway, a disruption of a gene encoding a ribulose-phosphate 3-epimerase and a disruption of a gene encoding a glucose-6-phosphate isomerase, and one or more overexpressed endogenous genes encoding an enzyme of the pentose phosphate pathway; and subjecting the yeast to evolutionary engineering on a medium comprising a hexose sugar and at least one pentose sugar, selecting for a yeast with improved growth rate when grown on a media comprising a hexose and at least one pentose sugar, so as to obtain an evolved yeast.