Methods, Apparatus, and Systems for Determining the Functional Microbial Niche and Identifying Interventions in Complex Hetergeneous Communities

A method for a design and intervention of a microbial consortia, comprising:

• a) identifying a particular task for the microbial consortia to modulate,
• b) identifying one or more members of the microbial consortia,
• c) measuring for one or more of the identified members a translational efficiency (TE) on genes and metabolic pathways, wherein the translational efficiency (TE) comprises genome annotation, transcription, translation, or a ratio of translation to transcription;
• d) categorizing the identified member into one or more guilds,
• e) identifying one or more microbial niches for each identified member,
• f) analyzing competition interactions between the identified members using distances between microbial niches and guild of members,
• g) designing an intervention that modulates the microbial consortia based on competition, guild association and niches, and
• h) modulating the microbial consortia.

A method for predicting an effect of perturbations on one or more members of a microbial consortia, comprising:

• a) identifying one or more members of the microbial consortia,
• b) measuring for one or more of the identified members a translational efficiency (TE) on genes and metabolic pathways, wherein the translational efficiency (TE) comprises genome annotation, transcription, translation, or a ratio of translation to transcription,
• c) categorizing the identified member into one or more guilds,
• d) identifying one or more microbial niches for each identified member,
• e) analyzing competition interactions between the identified members using distances between microbial niches and guild of members,
• f) predicting the effect of an intervention that modulates the microbial consortia based on competition, guild association and niches, and
• g) predicting the effect of an intervention that modulates a composition of the microbial consortia.

A method for selecting one or more members of a microbial consortia for a particular task, said method comprising:

• a) identifying one or more members of the microbial consortia,
• b) measuring for one or more of the identified members a translational efficiency (TE) on genes and metabolic pathways, wherein the translational efficiency (TE) comprises genome annotation, transcription, translation, or a ratio of translation to transcription,
• c) categorizing the identified member into one or more guilds,
• d) identifying one or more microbial niches for each identified member,
• e) analyzing competition interactions between the identified members using distances between microbial niches and guild of members,
• f) identifying one or more particular task to be performed by one or more members of the microbial consortia, and
• h) selecting one or more members of the microbial consortia based on the task to be performed.