Meet a resident of the biggest bacterial city in your house

Aeromonas Isolate Lab Report

Kyle Callegari

This study details physiological responses and genetic analysis of an isolated bacteria strain from a kitchen sponge. You will learn about a verity of selective and differential media’s as well as physiological tests to determine activity expressed genes of a bacterial culture.

Figure. The trials of isolating a pure bacterial strain.

Read the full report here

Reducing Allergic Reactions to Cheese

Title: Certain microbes may reduce allergy-like reactions in many people

Date: April 16, 2019


Researchers at Iowa State University are studying bacteria strains of the genus Brevibacterium that have genetic pathways to reduce histamine production.   Histamine is a compound involved in human immune response and around one present of people get allergy-like symptoms from the ingestion of it.   naturally forming biofilms of bacteria and fungi have been used in the cultivation of cheese for thousands of years.   These communities develop on the surface of the cheese and slowly form the rind of the cheese.   These communities are not well studied, and researchers lead by Stephan Schmitz-Esser are working to manipulate the fermenting communities to optimize the process and reduce the histamine production.

This was a well written article that communicated the issue effectively by explaining the cause and effects that lead to the study.   I found this article interesting because it divulged that there has not been a lot of research that has been done on the communities that comprise the fermentation of cheese products.   I find this surprising given it is a product we ingest, and we don’t even know the microbial composition of their processes.   Further research into the subject reviled that histamine formation is a huge product of cheese fermentation, but it can lead to histamine intoxication.   This can halt fermentation.   If conditions become toxic for fermenting species the entire process halts.   It turns out, the sole carbon source of the Brevibacterium species being studied is histamine!   This putative metabolic pathway for histamine degradation is critical for cheese ripening and solidifies Brevibacteriums importance.   This connects to our lessons of the fermentation process and the formation of bio-films.   The complexity of this community and the interdependence that makes their variety necessary is truly amazing.   I am curious how fungal species contribute to the rind forming biofilms?   I did not find anything about their role in the microbial community but would be interested to know more.


Ballads of Microbiology – Kyle Callegari

Oh Flagella


This piece is a word art poem.   The piece is informative about the use and range of flagella as a motile mechanism.   The poem depicts the run and tumble technique employed in the movement of microbes with flagella.   It does not touch on the use of membranous protein receptors in sensing temporal gradients, but rather how the cell responds to these gradients.   the piece is engaging with an audience prompting the reader to interact with the page.   For a viewer that is unfamiliar with flagella as a form of motility for microorganisms, the piece give them a visual representation that may further cue them into the intent of the piece.


Personifying Archaea

Consider the methanogen, who’s not at all a gentleman,

I know it is quite grim, but oxygen will kill him.

This bawdy life is not for most, the pace typically slows,

For this frowzy fellow will boast, foul smells satiate his nose.

So if he wants to live in mud, know that it is his lifeblood,

He only eats organic bud, if that’s not for you then move with scud.


Thermophiles won’t pander, their position is staunch and bold.

Speaking out with candor, they’re hyper sensitive to the cold.

While they will detest a chill, they thrive in what they know.

Be thankful you don’t share a bill, or need a hot tub to becalm and grow.

So if you see him wrapped up tight, coiled back to increase his might,

And it seems a wild sight, be understanding of his right.


The halophile seems whiney, although she’s really just precise.

You see she likes things briny, and doesn’t like to ask you twice.

Keeping balance does her well, you could learn a thing here, hun.

When things are going really swell, you’ll find her soaking up the sun.

So when the piquant señiorita, demands a saline margarita,


Just give her what she need-a, curacao will not please-a.

These lives are lived by a specialized few, but would not suit neither me nor you.

Drastic livings are what archaea do, so look at them, if you need an extreme view.


This poem personifies three of the major archaeal groups we have learned about.   It delves into the lifestyles and touches on adaptations that have allowed these phyla to thrive in such extreme niches.   The reader learns methanogens are anoxic,  it hints at their production of methane through energy metabolism, hints at the chemoorganotroph lifestyle they can live, and includes a little about the habitat you can find them in.   The reader learns hyperthermophiles excel in hot environments.   The poem alludes to heat shock proteins and positive supercoiling as well.   The reader learns halophiles prefer salty environments.   The poem also alludes to the use of potassium to maintain osmotic balance, and the use of a light mediated proton pump.


I am a fermenter


I am a fermenter,

If you want a nice wine,

You need only to ask,

I’ll make it quite fine,

Or at least it will pass.


I am a fermenter,

I will make you a beer,

I really don’t mind.

The recipe’s here,

It was easy to find.


I am a fermenter,

I can make you some cheese,

I will make it now,

If you will just stay, please.

It’s fresh from the cow!


I am a fermenter,

I’m fed on such rich food.

My home is a gut,

yet management seems rude.

I might leave out the butt.


This poem highlights products we consume and crucial habitats in which we benefit from the existence of fermenting microbes.   I feel the poem would be an excellent and fun learning tool in an elementary classroom.   It integrates literary and scientific concepts that would be efficient in a classroom setting.

A2: Social bacterium, M. xanthus cooperate when food is scarce

Article Title/Link and Date: A social bacterium with versatile habits – January 22, 2019

Source: ScienceDaily

Myxocoxxus xanthus is a particularly cooperative predatory species that swarm together hunting other microorganisms in the soil.   When food is scarce thousands aggregate in fruiting bodies and form resting spores, allowing them to withstand hunger and drought.   The study referenced in the article found a surprising amount of genetic diversity and social behavior within the species cooperative, which had previously been theorized to be socially ubiquitous.   The researchers isolated communities of common ancestors and noticed differences social behavior arising from mutations within the ancestrally separated communities.   Diversity appears to be frequent in bacterial social groups, and it is speculated diverse cooperatives are evolutionarily favored over homogeneous ones.

This journal article and study touches on a lot of topics we have discussed in class.   A single species conglomerate utilizing the motile mechanisms of pili, and secretory lubrication.   They are predatory heterotrophs, and the article discusses cooperative interactions within the species similar to bio-films or localizing human microbiomes.

We know secretory mobility is metabolically demanding and so the predatory cooperative must be effective hunters to sustain their lifestyle.   Studying the yellow fruiting bodies of the dormant species was an effective measure of social variability, but I found the results more exciting.   Understanding the extent of diversity within a phylogenetically limited community I think speaks volumes about genetic variability, and the fluidity of useful genes.

Bio-films are cooperatives of bacteria that conjoin to increase their chances of survival.   I am curious how this study could better inform bio-film interactions?   It would be interesting if a variety of species that serve the same functional role in the community were similar in diversity to a single species with a unified role.   This could reinforce the importance of gene expression over taxonomic classification.   This is merely wild speculation at this point.

Painting with Microbes

Extending an Olive Branch – Kyle Callegari, BIOL 342 Sec. 1


Johnny Bravo – Kyle Callegari, BIOL 342 Sec. 1


Yin Yang – Kyle Callegari, BIOL 342 Sec. 1


For the first bacteria plate, on TSA medium, my intent was solely to become more comfortable with streaking a design on a solid medium plate.   I tested adding varied amounts of bacteria and played around with the amount of strokes before swabbing for more bacteria.   I additionally became comfortable using the different sides of the inoculation loop for different width strokes.   The TSA medium is not differential or selective.

The Eosin methylene blue agar is a selective and differential medium used to culture gram-negative bacteria.   Johnny Bravo’s facial features grew a dark purple color indicating rapid lactose fermentation.   This bacteria produces acidic waste quickly and in turn absorbed the dark dye.   The tan strains have remained uncolored because they do not ferment lactose, but rather remove amino acid groups from the lactose medium increasing the pH. I used S. marcescens, and E. aerogenes on this plate My intent with this piece was was to create a recognizable figure that recalls fond memories.

The MacConkey agar is a selective and differential solid medium designed to isolate gram-negative bacteria.   It has dye that indicates the fermentation of lactose by turning pink when the process is occurring.   I used S. marcescens and C. freundii on this plate.   The yin yang symbol represents inseparable and contradictory opposites, and dates back to the third century.   It is possible S. marcescens has a faster growth rate than C. freundii, and that is why the bacteria in pink didn’t establish as well.

Epithet Epitaphs, Ernest L. Biberstien

The prokaryotic genus Bibersteinia is named after bacteriologist Ernest L. Biberstien. Biberstein did much of the early characterization of the species Bibersteinia trehalosi originally classified [Pasteurella] trehalosi. The species is a pathogen associated with pneumonia in sheep and systematic infections in lambs. The genus of this species is derivative of Biberstein’s last name, and the species name contains the Latin root hal- which can mean breath, most likely referring to its association with pneumonia in sheep. The discovery was made due to advancements in pathogenesis and epidemiology of the organism that allowed for a reclassification of the collection of strains identified as genus Pasteurella.   Biberstein characterized the serotyping scheme for the organism; sterotypes are district variations within a species of cell surface antigens. He also preformed some of the earliest DNA-DNA relatedness studies that indicated the unique nature of the taxon.


Blackall, P. J., Bojesen, A. M., Christensen, H., & Bisgaard, M. (2007). Reclassification of [Pasteurella] trehalosi as Bibersteinia trehalosi gen. nov., comb. nov. International Journal of Systematic and Evolutionary Microbiology, 57(4), 666-674.

Dassanayake, R. P.; Call, D. R.; Sawant, A. A.; Casavant, N. C.; Weiser, G. C.; Knowles, D. P.; Srikumaran, S. (2009). “Bibersteinia trehalosi Inhibits the Growth of Mannheimia haemolytica by a Proximity-Dependent Mechanism”. Applied and Environmental Microbiology. 76 (4): 1008—1013.

Parte, A. (n.d.). Genus Bibersteinia. Retrieved January 24, 2019, from

space microbes aren’t so alien after all

January 8, 2019

The link is to a great article about bacteria adapting to the harsh conditions of the International Space Station (ISS)!   There are thousands of different microbes in the ISS.   They all have mutated to cope with the stressful environment of space.   We have discussed the high mutation rate of bacteria in class and this is well illustrated through the study.

The study did a fine job of engaging the public by including rhetoric that captivates the public’s imagination. The article included reference to the study of bacteria in preparation for voyages to mars and subdued concern of any health risk in space bacteria could pose.   Additionally the author included many factors that could affect bacterial colonization, and posed questions and parameters a scientist would consider in studying bacteria in space.   The Author also used specific strands of bacteria to further inform readers.   I found the perimeters scientists thought may effect bacterial growth (radiation, microgravity, and lack of ventilation to be interesting.

I am curious to know more about the mutations these bacteria have undergone, and what selection pressures led to these mutations.

Ryan A. Blaustein, Alexander G. McFarland, Sarah Ben Maamar, Alberto Lopez, Sarah Castro-Wallace, Erica M. Hartmann.


Hey everyone my name is Kyle.   I am a junior at UAF studying Biology.   I enjoy reading, hiking, and playing ultimate Frisbee.   I am very interested in Microbiology because the field is unfamiliar to me.   Learning about organisms I have been unable to observe the majority of my life is intriguing, and I hope studying microorganisms will alter my approach to biological questions.