User:Jarle Pahr/Microbiology

Notes on microbiology:

http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0059310

Rapid microbiological methods: http://www.rapidmicrobiology.com/test-methods/Rapid-Method-Pharma.php

When Is a Microbial Culture “Pure”? Persistent Cryptic Contaminant Escapes Detection Even with Deep Genome Sequencing: http://mbio.asm.org/content/4/2/e00591-12.abstract

http://cellculture.bitesizebio.com/articles/cell-culture-passage-number-explained/

Concepts/Glossary

• Passage number
• SPANC balance: Balance between self-protection and nutritional capability.

Four heresies (see http://webspace.pugetsound.edu/facultypages/momartin/Micro/2008%20Micro%20lectures/Micro09.pdf)

• Phenotypic variation in wild-type vs lab strains. Continual cultivation is essentially a selective agent
• Biofilms as the natural state of microbes.
• Bacteria communicate and respond to population size and structure
• The great plating anomaly

Labs/research groups

Richard Lenski: http://myxo.css.msu.edu/

Strain collections

American Type Culture Collection (ATCC): http://www.lgcstandards-atcc.org/Products/Cells%20and%20Microorganisms/Primary%20Cells.aspx?geo_country=no

NCMA (Previously CCMP): https://ncma.bigelow.org/

Microbiology-themed blogs: http://www.microbe.net/microbiology-blogs/

World Federation for Culture Collections: http://www.wfcc.info/

Growth data

Growth data from cultures:

Strain/plasmid	Date	Volume	Medium	Container	Incubation conditions	Incubation time	OD600	# of samples used for measuring OD600	Comment
Dh5a:pJP-3	22.5.13	5 mL	LB + 50 ug/mL Kan	13 mL tube	37 C, 225 RPM	~ 13 h		1
BW27784	1.6.13	5 mL	LB	13 mL tube	37 C, 225 RPM	ON	7,7
BW27786	1.6.13	5 mL	LB	13 mL tube	37 C, 225 RPM	ON	2,9
BW27784	08.6.13	~3 mL	LB	13 mL tube	~20 C (on bench)	ON	0,9	1

Educational

http://invisiblelife.yourwildlife.org/

http://media.hhmi.org/biointeractive/vlabs/bacterial_id/index.html

Handbooks and references

http://kunde.datakvalitet.no/SIHF/Mikrobiologi/

Morphology

http://schaechter.asmblog.org/schaechter/2013/04/e-coli-cells-face-facs-and-get-back-into-shape.html

Blogs

http://microbepost.org

http://covertlab.stanford.edu/publicationpdfs/ChaosJKarr2013.pdf

microBEnet blog:

http://www.microbe.net/microbenet-blog/

Resources

http://www.microbelibrary.org/

Encyclopedia of Life: http://eol.org/

Links

http://www.earthmicrobiome.org/

http://www.microbemagazine.org/

http://www.microbe.net

http://www.microbeworld.org/

American society for Microbiology (ASM): www.asm.org

http://schaechter.asmblog.org/schaechter/2013/02/bacterial-antidepressants-avoiding-stationary-phase-stress.html

http://schaechter.asmblog.org/schaechter/2013/04/e-coli-cells-face-facs-and-get-back-into-shape.html

Protocol outline for sequencing of environmental isolates: http://www.microbe.net/2013/08/12/summary-of-undergraduate-genome-sequencing-project/

Culturing

http://schaechter.asmblog.org/schaechter/2010/07/the-uncultured-bacteria.html

The water agar test: a new test to measure the bacteriological quality of cream.: http://www.ncbi.nlm.nih.gov/pubmed/1097493

Bibliography

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12352.html

The last generation of bacterial growth in limiting nutrient A Bren, Y Hart, E Dekel, D Koster, U Alon - BMC systems biology, 2013

DNA signature-based approaches for bacterial detection and identification: http://www.sciencedirect.com/science/article/pii/S0048969708010838

Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4 : http://genomea.asm.org/content/1/2/e00086-13.full

http://link.springer.com/article/10.1007/s00284-013-0401-y

http://www.microbialcellfactories.com/content/7/1/31

Equipment

http://microbiologybuyersguide.com/

Software

http://weizhong-lab.ucsd.edu/cd-hit/

Journals

Microbiology: http://mic.sgmjournals.org/

BMC Microbiology

Molecular Microbiology

Journal of Bacteriology

INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLY

Journal of Experimental Microbiology and Immunology (JEMI): http://www.microbiology.ubc.ca/undergraduate/jemi

Mycoplasmas

http://mmbr.asm.org/content/62/4/1094.full

Books

Bergey's Manual of Systematic Bacteriology:

• Volume 1:
• Volume 2:
• Volume 3:
• Volume 4:

The Desk Encyclopedia of Microorganisms: http://www.amazon.com/Desk-Encyclopedia-Microbiology-Second-Edition/dp/0123749808

Brock's Microbiology

Microbiology: An evolving science.

Software

OpenCFU: http://sourceforge.net/projects/opencfu/?source=directory

Supplies

http://www.amazonsupply.com/microbiology-supplies/s/393446011/ref=gw_c_ls_ms